@article{lemey2010,
	title = {Phylogeography takes a relaxed random walk in continuous space and time},
	volume = {27},
	number = {8},
	journal = {Molecular Biology and Evolution},
	author = {Lemey, Philippe and Rambaut, Andrew and Welch, John J and Suchard, Marc A},
	year = {2010},
	note = {Publisher: SMBE},
	pages = {1877--1885},
}

@article{oliva19,
title={Accounting for ambiguity in ancestral sequencereconstruction},
author={Oliva, A and Pulicani, S and Lefort, V and Br\'eh\'elin, L. and Gascuel, O. and Guindon, S},
journal={Bioinformatics},
  pages={https://www.biorxiv.org/content/early/2018/09/05/409029},
year={2019}
}

@article{etheridge2008,
  title={Drift, draft and structure: some mathematical models of evolution},
  author={Etheridge, Alison M},
  journal={Banach Center Publ.},
  volume={80},
  pages={121--144},
  year={2008}
}

@inproceedings{berestycki2009,
  title={Survival, extinction and ergodicity in a spatially continuous population model},
  author={Berestycki, N and Etheridge, A and Hutzenthaler, M},
  booktitle={Markov Proc. Rel. Fields},
  year={2009}
}
@article{barton2010,
  title={A new model for evolution in a spatial continuum},
  author={Barton, NH and Etheridge, AM and V{\'e}ber, A},
  journal={Electronic Journal of Probability},
  volume={15},
  number={7},
  year={2010}
}

@article{barton2010b,
  title={A new model for extinction and recolonization in two dimensions: quantifying phylogeography},
  author={Barton, Nicholas H and Kelleher, Jerome and Etheridge, Alison M},
  journal={Evolution},
  volume={64},
  number={9},
  pages={2701--2715},
  year={2010},
  publisher={Wiley Online Library}
}
@article{veber2012,
author = {V{\'e}ber, A and Wakolbinger, A},
title = {The spatial {L}ambda-{F}leming-{V}iot process: an event-based construction and a lookdown representation},
year = {2014},
journal = {Annales de l'Institut Henri Poincar\'e},
pages={in press}
}

@article{tilman2011,
  title={Diversification, biotic interchange, and the universal trade-off hypothesis},
  author={D. Tilman},
  journal={The American Naturalist},
  volume={178},
  number={3},
  pages={355--371},
  year={2011},
  publisher={JSTOR}
}


@article{gernhard08,
  title={The conditioned reconstructed process},
  author={Gernhard, Tanja},
  journal={Journal of Theoretical Biology},
  volume={253},
  number={4},
  pages={769--778},
  year={2008},
  publisher={Elsevier}
}
@article{ayres12,
  title={BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics},
  author={Ayres, Daniel L and Darling, Aaron and Zwickl, Derrick J and Beerli, Peter and Holder, Mark T and Lewis, Paul O and Huelsenbeck, John P and Ronquist, Fredrik and Swofford, David L and Cummings, Michael P and others},
  journal={Systematic Biology},
  volume={61},
  number={1},
  pages={170--173},
  year={2012},
  publisher={Oxford University Press}
}

@article{ho11,
  title={Time-dependent rates of molecular evolution},
  author={Ho, Simon YW and Lanfear, Robert and Bromham, Lindell and Phillips, Matthew J and Soubrier, Julien and Rodrigo, Allen G and Cooper, Alan},
  journal={Molecular Ecology},
  volume={20},
  number={15},
  pages={3087--3101},
  year={2011},
  publisher={Wiley Online Library}
}


@article{fletcher10,
  title={The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection},
  author={Fletcher, William and Yang, Ziheng},
  journal={Molecular Biology and Evolution},
  volume={27},
  number={10},
  pages={2257--2267},
  year={2010},
  publisher={SMBE}
}


@article{degnan09,
  title={Gene tree discordance, phylogenetic inference and the multispecies coalescent},
  author={Degnan, J.H. and Rosenberg, N.A.},
  journal={Trends in Ecology \& Evolution},
  volume={24},
  number={6},
  pages={332--340},
  year={2009},
  publisher={Elsevier}
}
@article{best,
  title={{BEST}: Bayesian estimation of species trees under the coalescent model},
  author={Liu, L.},
  journal={Bioinformatics},
  volume={24},
  number={21},
  pages={2542--2543},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{lg4x,
  title={Modeling protein evolution with several amino acid replacement matrices depending on site rates},
  author={Le, Si Quang and Dang, Cuong Cao and Gascuel, Olivier},
  journal={Molecular Biology and Evolution},
  volume={29},
  number={10},
  pages={2921--2936},
  year={2012},
  publisher={SMBE}
}
@article{stem,
  title={{STEM}: species tree estimation using maximum likelihood for gene trees under coalescence},
  author={Kubatko, L.S. and Carstens, B.C. and Knowles, L.L.},
  journal={Bioinformatics},
  volume={25},
  number={7},
  pages={971--973},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{startbeast,
  title={Bayesian inference of species trees from multilocus data},
  author={Heled, J. and Drummond, A.J.},
  journal={Molecular Biology and Evolution},
  volume={27},
  number={3},
  pages={570--580},
  year={2010},
  publisher={SMBE}
}

@article{guindon10,
  title={Bayesian estimation of divergence times from large sequence alignments},
  author={Guindon, St{\'e}phane},
  journal={Molecular Biology and Evolution},
  volume={27},
  number={8},
  pages={1768--1781},
  year={2010},
  publisher={SMBE}
}

@article{guindon18,
  title={Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a ``Doubly Intractable'' Problem},
  author={Guindon, St{\'e}phane},
  journal={Systematic Biology},
  volume={67},
  number={},
  pages={651-661},
  year={2018},
}


%% Created for guindon at 2009-04-21 13:11:50 +1200 

@article{soubrier12,
  title={The influence of rate heterogeneity among sites on the time dependence of molecular rates},
  author={Soubrier, J. and Steel, M. and Lee, M.S.Y. and Sarkissian, C.D. and Guindon, S. and Ho, S.Y.W. and Cooper, A.},
  journal={Molecular Biology and Evolution},
  year={2012},
  publisher={SMBE}
}

%% Saved with string encoding Unicode (UTF-8) 
@article{matsen07,
  title={Phylogenetic mixtures on a single tree can mimic a tree of another topology},
  author={Matsen, F.A. and Steel, M.},
  journal={Systematic Biology},
  volume={56},
  number={5},
  pages={767--775},
  year={2007},
  publisher={Oxford University Press}
}
@book{bailey64,
  title={The elements of stochastic processes with applications to the natural sciences},
  author={Bailey, Norman TJ},
publisher={Wiley},
  year={1964}
}

@article{lemey2009,
  title={Bayesian phylogeography finds its roots},
  author={Lemey, Philippe and Rambaut, Andrew and Drummond, Alexei J and Suchard, Marc A},
  journal={PLoS Comput Biol},
  volume={5},
  number={9},
  pages={e1000520},
  year={2009},
  publisher={Public Library of Science}
}

@article{gillespie2011,
  title={Long-distance dispersal: a framework for hypothesis testing},
  author={Gillespie, R.G. and Baldwin, B.G. and Waters, J.M. and Fraser, C.I. and Nikula, R. and Roderick, G.K.},
  journal={Trends in Ecology \& Evolution},
  year={2011},
  vol=27,
  pages={47,56}
}

@article{guindon13,
  title={From trajectories to averages: an improved description of the heterogeneity of substitution rates along lineages.},
  author={Guindon, S.},
  journal={Systematic Biology},
  year={2013},
volume={62},
pages={22-34},
  publisher={Oxford University Press}
}

@article{arnold01,
Author = {Barry C. Arnold and Enrique Castillo and Jose Maria Sarabia},
Title = {Conditionally Specified Distributions: An Introduction},
Journal = {Statistical Science},
Year = 2001,
Volume = 16,
Pages = {249,265}
}

@article{arnold07,
	Author = {Barry C. Arnold and Enrique Castillo and Jose Maria Sarabia},
	Date-Added = {2009-04-21 13:08:07 +1200},
	Date-Modified = {2009-04-21 13:11:32 +1200},
	Journal = {Journal of Statistical Planning and Inference},
	Pages = {3249-3260},
	Read = {Yes},
	Title = {Variations on the classical multivariate normal theme},
	Volume = {137},
	Year = {2007},
	Bdsk-File-1 = { }}


@article{boussau06,
  title={Efficient likelihood computations with nonreversible models of evolution},
  author={Boussau, Bastien and Gouy, Manolo},
  journal={Systematic biology},
  volume={55},
  number={5},
  pages={756--768},
  year={2006},
  publisher={Oxford University Press}
}

@article{boussau08,
	Abstract = {Fossils of organisms dating from the origin and diversification of cellular life are scant and difficult to interpret, for this reason alternative means to investigate the ecology of the last universal common ancestor (LUCA) and of the ancestors of the three domains of life are of great scientific value. It was recently recognized that the effects of temperature on ancestral organisms left 'genetic footprints' that could be uncovered in extant genomes. Accordingly, analyses of resurrected proteins predicted that the bacterial ancestor was thermophilic and that Bacteria subsequently adapted to lower temperatures. As the archaeal ancestor is also thought to have been thermophilic, the LUCA was parsimoniously inferred as thermophilic too. However, an analysis of ribosomal RNAs supported the hypothesis of a non-hyperthermophilic LUCA. Here we show that both rRNA and protein sequences analysed with advanced, realistic models of molecular evolution provide independent support for two environmental-temperature-related phases during the evolutionary history of the tree of life. In the first period, thermotolerance increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and of Archaea-Eukaryota; in the second period, it decreased. Therefore, the two lineages descending from the LUCA and leading to the ancestors of Bacteria and Archaea-Eukaryota convergently adapted to high temperatures, possibly in response to a climate change of the early Earth, and/or aided by the transition from an RNA genome in the LUCA to organisms with more thermostable DNA genomes. This analysis unifies apparently contradictory results into a coherent depiction of the evolution of an ecological trait over the entire tree of life.},
	Address = {Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite de Lyon, Universite Lyon I, 43 Boulevard du 11 Novembre, 69622 Villeurbanne, France.},
	Au = {Boussau, B and Blanquart, S and Necsulea, A and Lartillot, N and Gouy, M},
	Author = {Boussau, Bastien and Blanquart, Samuel and Necsulea, Anamaria and Lartillot, Nicolas and Gouy, Manolo},
	Crdt = {2008/11/28 09:00},
	Da = {20081218},
	Date-Added = {2009-01-30 16:18:39 +1300},
	Date-Modified = {2009-01-30 16:18:57 +1300},
	Dcom = {20090113},
	Dep = {20081126},
	Doi = {10.1038/nature07393},
	Edat = {2008/11/28 09:00},
	Issn = {1476-4687 (Electronic)},
	Jid = {0410462},
	Journal = {Nature},
	Jt = {Nature},
	Language = {eng},
	Mh = {Adaptation, Physiological/genetics/*physiology; Archaea/genetics/*physiology; Evolution, Molecular; Genes, rRNA/genetics; *Hot Temperature; Phylogeny},
	Mhda = {2009/01/14 09:00},
	Number = {7224},
	Own = {NLM},
	Pages = {942--945},
	Phst = {2008/03/05 {$[$}received{$]$}; 2008/09/01 {$[$}accepted{$]$}; 2008/11/26 {$[$}aheadofprint{$]$}},
	Pii = {nature07393},
	Pl = {England},
	Pmid = {19037246},
	Pst = {ppublish},
	Pt = {Journal Article; Research Support, Non-U.S. Gov't},
	Sb = {IM},
	So = {Nature. 2008 Dec 18;456(7224):942-5. Epub 2008 Nov 26. },
	Stat = {MEDLINE},
	Title = {Parallel adaptations to high temperatures in the Archaean eon.},
	Volume = {456},
	Year = {2008 Dec 18},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature07393}}

@article{dereeper08,
	Abstract = {Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The 'One Click' mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The 'Advanced' mode uses the same pipeline but allows the parameters of each program to be customized by users. The 'A la Carte' mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/},
	Author = {Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O.},
	Date-Added = {2009-01-19 17:02:10 +1300},
	Date-Modified = {2009-01-19 17:03:31 +1300},
	Journal = { Nucleic Acids Res.},
	Title = {Phylogeny.fr: robust phylogenetic analysis for the non-specialist.},
	Volume = {36},
	Year = {2008}}

@article{lartillot06,
	Author = {Nicolas Lartillot},
	Date-Added = {2008-12-18 09:36:03 +1300},
	Date-Modified = {2008-12-18 09:39:29 +1300},
	Journal = {Journal of Computational Biology},
	Pages = {1701-1722},
	Rating = {5},
	Title = {Conjugate Gibbs Sampling for Bayesian Phylogenetic Models },
	Volume = {13},
	Year = {2006},
	Bdsk-File-1 = { }}

@book{aarts97,
	Address = {Chichester},
	Author = {E. Aarts and J. K. Lenstra},
	Publisher = {Wiley},
	Title = {Local search in combinatorial optimization},
	Year = 1997}

@article{abascal05,
	Author = {F. Abascal and R. Zardoya and D. Posada},
	Journal = {Bioinformatics},
	Pages = {2104-2105},
	Title = {ProtTest: selection of best-fit models of protein evolution},
	Volume = 21,
	Year = {2005}}

@phdthesis{adachi95,
	Author = {J. Adachi},
	School = {The Graduate University for Advanced Studies},
	Title = {Modeling of Molecular Evolution and Maximum Likelihood Inference of Molecular Phylogeny},
	Year = 1995}

@article{akaike74,
	Author = {H. Akaike},
	Journal = {IEEE Transactions on Automatic Control},
	Pages = {716-723},
	Title = {A new look at the statistical model identification},
	Volume = 19,
	Year = {1974}}

@article{amrine03,
	Author = {H. Amrine-Madsen and K Koepfli and R. Wayne and M. Springer},
	Journal = {Molecular Phylogenetics and Evolution},
	Pages = {225-240},
	Title = {A new phylogenetic marker, apolipoprotein {B}, provides compelling evidence for eutherian relationships},
	Volume = 28,
	Year = {2003}}

@article{ane05,
	Author = {C. An\'e and J. Burleigh and M. McMahon and M. Sanderson},
	Journal = {Molecular Biology and Evolution},
	Pages = {914-924},
	Title = {Covarion structure in plastid genome evolution: a new statistical test},
	Volume = 22,
	Year = {2005}}

@article{anisimova01,
	Author = {M. Anisimova and J. Bielawski and Z. Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {1585-1592},
	Title = {The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites},
	Volume = 18,
	Year = {2001}}

@article{anisimova02,
	Author = {M. Anisimova and J. Bielawski and Z. Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {950-958},
	Title = {Accuracy and power of Bayes prediction of amino acid under positive selection},
	Volume = 19,
	Year = {2002}}

@article{anisimova03,
	Author = {M. Anisimova and R. Nielsen and Z. Yang},
	Journal = {Genetics},
	Pages = {1229-1236},
	Title = {Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.},
	Volume = 164,
	Year = {2003}}

@article{anisimova06,
	Author = {M. Anisimova and O. Gascuel},
	Journal = {Systematic Biology},
	Pages = {539-552},
	Title = {Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative},
	Volume = 55,
	Year = {2006}}

@article{anisimova07,
  title={Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites},
  author={Anisimova, Maria and Yang, Ziheng},
  journal={Molecular Biology and Evolution},
  volume={24},
  number={5},
  pages={1219--1228},
  year={2007},
  publisher={SMBE}
}

@article{anisimova11,
  title={Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes},
  author={Anisimova, M. and Gil, M. and Dufayard, J.F. and Dessimoz, C. and Gascuel, O.},
  journal={Systematic Biology},
  volume={60},
  number={5},
  pages={685--699},
  year={2011},
  publisher={Oxford University Press}
}



@article{atv,
	Author = {C. Zmasek and S. Eddy},
	Journal = {Bioinformatics},
	Pages = {383-384},
	Title = {{ATV}: display and manipulation of annotated phylogenetic trees},
	Volume = 17,
	Year = 2001}



@book{intro-algo,
	Author = {T. H. Cormen and C. E. Leiserson and R. L. Rivest},
	Chapter = { 17 greedy algorithms},
	Pages = {329-356},
	Publisher = {The Massachuset Institute of Technology Press},
	Title = {Introduction to algorithms},
	Year = 1992}

@article{seqgen,
	Author = {A. Rambaut and N.C. Grassly},
	Journal = {Computer Applications in the Biosciences (CABIOS)},
	Pages = {235-238},
	Title = {{S}eq-{G}en: an application for the {M}onte {C}arlo simulation of {DNA} sequence evolution along phylogenetic trees.},
	Volume = 13,
	Year = 1997}

@article{bailey02,
	Author = {J. Bailey and Z. Gu and R. Clark and K. Reinert and R. Samonte and S. Schwartz and M. Adams and E. Myers and P. Li and E. Eicher},
	Journal = {Science},
	Pages = {1003-1007},
	Title = {Recent segmental duplications in the human genome},
	Volume = 297,
	Year = 2002}

@article{baele06,
	Author = {G. Baele and J. Raes and Y. Van de Peer and S. Vansteelandt},
	Journal = {Molecular Biology and Evolution},
	Pages = {1397-1405},
	Title = {An improved statistical method for detecting heterotachy in nucleotide sequences},
	Volume = 23,
	Year = 2006}

@article{berry,
	Author = {V. Berry and O. Gascuel},
	Journal = {Theoretical Computer Science ({\`a} paraitre)},
	Title = {Inferring evolutionary trees with strong combinatorial confidence.},
	Year = 2000}

@article{kumar02,
	Author = {S. Kumar and S. Subramanian},
	Journal = {PNAS},
	Pages = {803-808},
	Title = {Mutation rates in mammalian genomes},
	Volume = {99},
	Year = {2002}}

@article{kumar96,
	Author = {Sudhir Kumar},
	Journal = {Molecular Biology and Evolution},
	Title = {A Stepwise Algorithm for Finding Minimum Evolution Trees},
	Year = 1996}

@article{nei97,
	Author = {Masatoshi Nei, Sudhir Kumar, and Kei Takahashi},
	Journal = {Special series of inaugural articles by members of the national academy of science},
	Pages = {584-593},
	Title = {The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids is small},
	Volume = 13,
	Year = 1997}

@article{nei98,
	Author = {M. Nei and S. Kumar and K. Takahashi},
	Journal = {PNAS},
	Pages = {12390-12397},
	Title = {The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small},
	Volume = 95,
	Year = 1998}

@inproceedings{abf96,
	Author = {R. Agarwala and V. Bafna and M. Farach and B. Narayanan                   and M. Paterson and M. Thorup},
	Booktitle = {Proceedings of the 7th Annual ACM-SIAM                    Symposium on Discrete Algorithms},
	Title = {On the approximability of numerical taxonomy:                   Fitting distances by tree metrics},
	Year = 1996}

@article{adell94,
	Author = {J. Adell and J. Dopazo},
	Journal = {Journal of Molecular Evolution},
	Pages = {305-309},
	Title = {{M}onte {C}arlo Simulation in phylogenies : An     application to Test the Constancy of Evolutionary Rates},
	Volume = 38,
	Year = 1994}

@incollection{adachi96,
	Address = {Tokyo},
	Author = {J. Adachi and M. Hasegawa},
	Booktitle = {Computer Science Monographs},
	Editor = {M. Ishiguro and G. Kitagawa and Y. Ogata and H. Takagi and Y. Tamura and T. Tsuchiya},
	Number = {28},
	Publisher = {The Institute of Statistical Mathematics},
	Title = {{MOLPHY} Version 2.3. Programs for molecular phylogenetics based on maximum likelihood},
	Year = 1996}

@article{adachi00,
	Author = {J. Adachi and Waddell P. and W. Martin and M. Hasegawa},
	Journal = {Journal of Molecular Evolution},
	Pages = {348-358},
	Title = {Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast {DNA}},
	Volume = 50,
	Year = 2000}

@article{almagor83,
	Author = {Hagai Almagor},
	Journal = {Journal of Theorical Biology},
	Note = {{I}nfluence du {V}oisinage sur l'{E}volution d'une     {S{\'e}}quence d'{ADN}},
	Pages = {633-645},
	Title = { A Markov analysis of {DNA} sequences},
	Utilisateur = {Guillaume Andrieu},
	Volume = 104,
	Year = 1983}

@book{alon92,
	Address = {Chichester},
	Author = {N. Alon and J.H. Spencer},
	Publisher = {Wiley},
	Title = {The Probabilistic Method},
	Year = 1992}

@dea{andrieu92,
	Address = {Montpellier},
	Author = {Guillaume Andrieu},
	School = {{E}cole {N}ationale {S}up{\'e}rieure {A}gronomique de {M}ontpellier},
	Title = {{M}od{\`e}les {P}robabilistes de {C}onstruction des {A}rbres  {P}hylog{\'e}n{\'e}tique},
	Utilisateur = {Gilles Caraux},
	Year = 1992}

@phdthesis{andrieu97,
	Author = {G. Andrieu},
	Month = {d{\'e}cembre},
	School = {Univ. Montpellier II},
	Title = {Estimation par intervalle d'une distance {\'e}volutive},
	Year = 1997}

@article{arisbrosou02,
	Author = {S. Aris-Brosou and Z. Yang},
	Journal = {Systematic Biology},
	Pages = {703-714},
	Title = {Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan {18S} ribosomal {RNA} phylogeny},
	Volume = 51,
	Year = 2002}

@book{atlan,
	Address = {Petaouchnok},
	Author = {Henri Atlan},
	Publisher = {Herman},
	Title = {L'organisation Biologique et la th{\'e}orie de l'information},
	Year = 1992}

@misc{atteson96,
	Author = {K. Atteson},
	Howpublished = {DIMACS},
	Month = {november},
	Title = {Workshop on Mathematical Hierarchies and Biology},
	Year = 1996}

@incollection{atteson97,
	Author = {K. Atteson},
	Booktitle = {Mathematical Hierarchies and Biology},
	Editor = {B. Mirkin and F.R. McMorris and F.S. Roberts and A. Rhzetsky},
	Pages = {133-148},
	Publisher = {American Mathematical Society},
	Title = {The performance of the {NJ} method of phylogeny reconstruction},
	Year = 1997}

@article{bailly03,
	Author = { X. Bailly and R. Leroy and S. Carney and O. Collin and F. Zal and A. Toulmond and D. Jollivet},
	Journal = {PNAS},
	Pages = {5885-5890},
	Title = {The loss of the hemoglobin \hbox{H$_2$S}-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by {D}arwinian positive selection},
	Volume = 1000,
	Year = 2003}

@article{bd86,
	Author = {H-J. Bandelt and A. Dress},
	Journal = {Advances in Applied Mathematics},
	Pages = {309-343},
	Title = {Reconstructing the Shape of a Tree from Observed     Dissimilarity Data},
	Utilisateur = {Vincent},
	Volume = 7,
	Year = 1986}

@misc{bandelt90,
	Author = {H.-J. Bandelt and A. von Haeseler and A. Bolick and                   H. Sch{\"u}tte},
	Howpublished = {preprint},
	Title = {A comparative study of sequence dissimilarities and                    evolutionnary distances derived from sets of aligned                    RNA sequences},
	Year = 1990}

@article{bandelt92,
	Author = {H.-J. Bandelt and A. Dress},
	Journal = {Advances Math.},
	Pages = {47-105},
	Title = {A canonical decomposition theory for metrics on a finite set},
	Volume = 92,
	Year = 1992}

@article{bandelt92b,
	Author = {H.-J. Bandelt and A. Dress},
	Journal = {Molecular Biology and Evolution},
	Pages = {242-252},
	Title = {Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data},
	Volume = 1,
	Year = 1992}

@article{barry87,
	Author = {Daniel Barry and J. A. Hartigan},
	Journal = {Biometrics},
	Pages = {261-276},
	Title = {Asynchronous Distance Between Homologous {DNA} Sequences},
	Volume = 43,
	Year = 1987}

@article{barry872,
	Author = {Daniel Barry and J. A. Hartigan},
	Journal = {Statistical Science},
	Pages = {191-210},
	Title = {Statistical Analysis of Homimoid Molecular Evolution},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Volume = 2,
	Year = 1987}

@article{barton2013,
  title={Modelling evolution in a spatial continuum},
  author={Barton, NH and Etheridge, AM and V{\'e}ber, A},
  journal={Journal of Statistical Mechanics: Theory and Experiment},
  volume={2013},
  number={01},
  pages={P01002},
  year={2013},
  publisher={IOP Publishing}
}


@inproceedings{barthelemy84,
	Address = {La Grande-Motte},
	Author = {J.-P. Barth{\'e}lemy and N.X. Luong},
	Booktitle = {Colloque ASSU.},
	Title = {Repr{\'e}sentations arbor{\'e}es de mesures de dissimilarit{\'e}},
	Year = 1984}

@book{barthelemy88,
	Author = {J.-P. Barth{\'e}lemy and Alain Gu{\'e}noche},
	Publisher = {Masson},
	Series = {{M}{\'e}thodes + {P}rogrammes},
	Title = {Les arbres et les repr{\'e}sentations des proximit{\'e}s},
	Year = 1988}

@article{barth88,
	Author = {J. P. Barth{\'e}lemy},
	Journal = {Journal of Classification},
	Pages = {229-236},
	Title = {Thresholded consensus for n-trees},
	Utilisateur = {Gilles Caraux and Olivier Gascuel},
	Volume = 5,
	Year = 1988}

@article{bazykin04,
	Author = {G. Bazykin and F. Kondrashov and A. Ogurtsov and S. Sunyaev and A. Kondrashov},
	Journal = {Nature},
	Pages = {558-562},
	Title = {Positive selection at sites of multiple amino acid replacements since rat-mouse divergence.},
	Volume = 3,
	Year = 2004}

@book{barthelemy91,
	Author = {J.P. Barth{\'e}lemy and A. Gu{\'e}noche},
	Editor = {Chichester},
	Publisher = {Wiley},
	Title = {Trees and proximities representations},
	Year = 1991}

@article{benjamini95,
	Author = {Y. Benjamini and Y. Hochberg},
	Journal = {Journal of the Royal Statistics Society: Series B (Statistical Methodology)},
	Pages = {289-300},
	Title = {Controlling the false discovery rate -- a practical and powerful approach to multiple testing},
	Volume = {57},
	Year = {1995}}

@article{benjamini00,
	Author = {Y. Benjamini and Y. Hochberg},
	Journal = {Journal of Educational and Behavioral Statistics},
	Pages = {60-83},
	Title = {The adaptive control of the false discovery rate in multiple hypothesis testing with independent statistics},
	Volume = {25},
	Year = {2000}}

@article{benjamini01,
	Author = {Y. Benjamini and D. Yekutieli},
	Journal = {Annals of Statistics},
	Pages = {1165-1188},
	Title = {The control of the false discovery rate in multiple testing under dependency},
	Volume = {29},
	Year = {2001}}

@inbook{benzecri,
	Address = {Paris},
	Author = {J. P. Benzecri},
	Chapter = {TIB No 3},
	Pages = {119-152},
	Publisher = {Dunod},
	Series = {L'analyse des donn{\'e}es},
	Title = {Description math{\'e}matique des classifications},
	Utilisateur = {Gilles Caraux},
	Volume = {I~: La Taxinomie},
	Year = 1973}

@article{benzer61,
	Author = {S. Benzer},
	Journal = {PNAS},
	Pages = {403-415},
	Title = {On the topography of genetic fine structure},
	Volume = 47,
	Year = 1961}

@phdthesis{berrythese,
	Author = {V. Berry},
	Month = {d{\'e}cembre},
	School = {Univ. Montpellier II},
	Title = {M{\'e}thodes et algorithmes pour reconstruire les arbres de l'{\'e}volution},
	Year = 1997}

@book{berge70,
	Author = {C. Berge},
	Publisher = {Dunod},
	Title = {Graphes et hypergraphes},
	Year = 1970}

@article{bertrand04,
	Author = {D. Bertrand and O. Gascuel},
	Journal = {WABI},
	Title = {Topological rearrangements and local search method for tandem duplication trees},
	Year = 2004}

@article{bertrand05,
	Author = {D. Bertrand and O. Gascuel},
	Journal = {{IEEE} Transactions on computational biology and bioinformatics},
	Title = {Topological rearrangements and local search method for tandem duplication trees},
	Volume = {2},
        Issue = {1},
	Year = 2005}

@article{bg96_boot,
	Author = {V. Berry and O. Gascuel},
	Journal = {Molecular Biology and Evolution},
	Pages = {999-1011},
	Title = {On the interpretation of Bootstrap trees:                   appropriate threshold of clade selection and induced                   gain},
	Volume = 13,
	Year = 1996}

@techreport{bg96_quad,
	Author = {V. Berry and O. Gascuel},
	Institution = {LIRMM},
	Month = {july},
	Number = {96-044},
	Title = {A quartet-based heuristics for phylogeny reconstruction},
	Year = 1996}

@inbook{bhattacharya,
	Address = {New York},
	Author = {Rabi N. Bhattacharya and Edwards C. Waymire},
	Chapter = { No IV Continuous-Parameter {M}arkov chains},
	Pages = {261-366},
	Publisher = {Wiley},
	Title = {Stochastic processes with applications},
	Utilisateur = {Guillaume Andrieu},
	Year = 1990}

@article{bielawski01,
	Author = {J. Bielawski and Z. Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {523-529},
	Title = {Positive and negative selection in the {\uppercase{\it{DAZ}}} gene family},
	Volume = {18},
	Year = 2001}

@article{bielawski03,
	Author = {J. Bielawski and Z. Yang},
	Journal = {Journal of Structural and Functional Genomics},
	Pages = {201-212},
	Title = {Maximum likelihood methods for detecting adaptive evolution after gene duplication},
	Volume = {3},
	Year = 2003}

@article{bielawski04,
	Author = {J. Bielawski and Z. Yang},
	Journal = {Journal of Molecular Evolution},
	Pages = {121-132},
	Title = {A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution},
	Volume = {59},
	Year = 2004}

@article{bishop85,
	Author = {M. J. Bishop and A. E. Friday},
	Journal = {Proceeding of the Royal Society of London},
	Pages = {271-302},
	Title = {{E}volutionary trees from nucleic acid and protein sequences},
	Utilisateur = {Guillaume Andrieu},
	Volume = {B 226},
	Year = 1985}

@article{blaisdell85,
	Author = {B. Edwin Blaisdell},
	Journal = {Journal of Molecular Evolution},
	Note = {{I}nfluence du {V}oisinage sur l'{E}volution d'une     {S{\'e}}quence d'{ADN}},
	Pages = {278-288},
	Title = {Markov chain analysis find a significant influence of neighboring bases on the occurence of a base in eucaryotic nuclear {DNA} sequences both  protein-coding and noncoding},
	Utilisateur = {Guillaume Andrieu},
	Volume = 21,
	Year = 1985}

@article{blaisdell91,
	Author = {Edwin Blaisdell},
	Journal = {Journal of Molecular Evolution},
	Pages = {521-528},
	Title = {average values of a dissimilarity measure not requiring sequence alignment are twice the average of conventional mismatch counts requiring sequence alignment for a variety of computer-Generated model systems},
	Utilisateur = {G. Andrieu},
	Volume = 32,
	Year = 1991}

@article{blake92,
	Author = {R.D. Blake and Samuel T. Hess and Janice Nicholson-Tuell},
	Journal = {Journal of Molecular Evolution},
	Note = {{I}nfluence du {V}oisinage sur l'{E}volution d'une     {S{\'e}}quence d'{ADN}},
	Pages = {189-200},
	Title = {The Influence of Nearest Neighbors on the Rate and Pattern of Spontaneous Point Mutations},
	Utilisateur = {Guillaume Andrieu},
	Volume = 34,
	Year = 1992}

@article{blanken82,
	Author = {Roger L. Blanken and Lynn C. Klotz and Alan G. Hinnebusch},
	Journal = {Journal of Molecular Evolution},
	Pages = {9-19},
	Title = {Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data},
	Utilisateur = {Gilles Caraux},
	Volume = 19,
	Year = 1982}

@article{blast,
	Author = {S. Altschul and W. Gish and W. Miller and  E. Myers and D. Lipman},
	Journal = {Journal of Molecular Biology},
	Pages = {403-410},
	Title = {Basic local alignment search tool},
	Volume = {215},
	Year = {1990}}

@article{bledsoe90,
	Author = {Anthony H. Bledsoe and Robert J. Raikow },
	Journal = {Journal of Molecular Evolution},
	Pages = {247-259},
	Title = {A quantitative assessment of congruence  between molecular and nonmolecular estimates of phylogeny},
	Utilisateur = {G. Andrieu},
	Volume = 30,
	Year = 1990}

@article{brauer02,
	Author = { M.J. Brauer and M.T. Holder and L.A. Dries and D.J. Zwickl and P.O. Lewis and D.M. Hillis},
	Journal = {Molecular Biology and Evolution},
	Pages = {1717-1726},
	Title = {Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference},
	Volume = 19,
	Year = 2002}

@book{breiman84,
	Author = {L. Breiman and J.H. Friedman and A. Olshen and Stone C.J.},
	Editor = {Belmont},
	Publisher = {Wadsworth},
	Title = {Classification and regression trees},
	Year = 1984}

@article{bremer88,
	Author = {K. Bremer},
	Journal = {Evolution},
	Note = {Donne une bonne facon de tester la robustesse d'un     arbre infere par une meth de parcimonie : faire un     arbre de consensus strict pr les arbres de valeur     opt, puis un avec aussi ceux de val opt+1,... et     noter a quelle etape disparait chq noeud},
	Pages = {795-803},
	Title = {The limits of amino acid sequence data in angiosperm     phylogenetic reconstruction},
	Utilisateur = {Vincent},
	Volume = 42,
	Year = 1988}

@book{brent73,
	Author = {R. Brent},
	Chapter = {5},
	Publisher = {Prentice-Hall},
	Title = {Algorithms for minimization without derivatives},
	Year = 1973}

@article{brossier85,
	Author = {Gildas Brossier},
	Journal = {Math. Sci. hum.},
	Pages = {5-21},
	Title = {Approximation des dissimilarit{\'e}s par des arbres additifs},
	Utilisateur = {Gilles Caraux},
	Volume = 91,
	Year = 1985}

@article{brown99,
	Author = {K. S. Brown},
	Journal = {Science},
	Pages = {990-991},
	Title = {Deep Green Rewrites Evolutionary History of Plants},
	Volume = 285,
	Year = 1999}

@article{bruno00,
	Author = {W. Bruno and N. Socci and A. Halpern},
	Journal = {Molecular Biology and Evolution},
	Pages = {189-197},
	Title = {Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction},
	Volume = 17,
	Year = 2000}

@incollection{bryant05,
	Address = {Oxford},
	Author = {D. Bryant and N. Galtier and M.-A. Poursat},
	Booktitle = {Mathematics of Evolution \& Phylogenetics},
	Editor = {O. Gascuel},
	Pages = {33-62},
	Publisher = {Oxford University Press},
	Title = {Likelihood Calculations in Phylogenetics},
	Year = 2005}

@article{weighbor,
	Author = {W. Bruno and N. D. Socci and A. L. Halpern},
	Journal = {Molecular Biology and Evolution},
	Pages = {189-197},
	Title = {Weighted Neighbor Joining: A Likelihood-based Approach to Distance-Based Phylogeny Reconstruction},
	Volume = 17,
	Year = 2000}

@article{buckley01,
	Author = {Thomas R. Buckley and Chris Simon and Geoffrey K. Chambers},
	Journal = {Systematic Biology},
	Pages = {67-86},
	Title = {Exploring Among-Site Rate Variation Models in a Maximum Likelihood Framework Using Empirical Data: Effects of Model Assumptions on Estimates of Topology, Branch Lengths, and Bootstrap Support},
	Volume = 50,
	Year = 2001}

@article{buckley01b,
	Author = {Thomas R. Buckley and Chris Simon and Hidetoshi Shimodaira and Geoffrey K. Chambers},
	Journal = {Molecular Biology and Evolution},
	Pages = {223-234},
	Title = {Evaluating Hypotheses on the Origin and Evolution of the New Zealand Alpine Cicadas (Maoricicada) Using Multiple-Comparison Tests of Tree Topology},
	Volume = 18,
	Year = 2001}

@article{bulmer91,
	Author = {Michael Bulmer},
	Journal = {Molecular Biology and Evolution},
	Pages = {868-883},
	Title = {Use of the method of generalized least squares in reconstructing phylogenies from sequence data},
	Volume = 8,
	Year = 1991}

@inbook{buneman71,
	Author = {P. Buneman},
	Chapter = {The recovery of trees from measures of dissimilarity},
	Pages = {387-395},
	Publisher = {Edhinburgh University Press},
	Title = {Mathematics in Archeological and Historical Sciences},
	Year = 1971}

@article{buneman74,
	Author = {P. Buneman},
	Journal = {J. of Comb. Theory},
	Pages = {48-50},
	Title = {A note on metric properties of trees},
	Volume = 17,
	Year = 1974}

@article{cao98,
	Author = {Y. Cao and A. Janke and P. Waddell and M. Westerman and O. Takenaka and S. Murata and N. Okada and S. Paabo and M. Hasegawa},
	Journal = {Journal of Molecular Evolution},
	Pages = {307-322},
	Title = {Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders},
	Volume = 47,
	Year = 1998}

@article{carroll76,
	Author = {J. Douglas Carroll},
	Journal = {Psychometrika},
	Pages = {439-463},
	Title = {Spatial, non-spatial and hybrid models for scaling},
	Utilisateur = {Gilles Caraux},
	Volume = 41,
	Year = 1976}

@article{cavalli67,
	Author = {L. L. Cavalli-Sforza and A. W. F. Edwards},
	Journal = {The American Journal of Human Genetics},
	Pages = {233-257},
	Title = {Phylogenetic analysis models and estimation procedures},
	Volume = 19,
	Year = 1967}

@article{cavender78,
	Author = {J. A. Cavender},
	Journal = {Mathematical Biosciences},
	Pages = {271-280},
	Title = {Taxonomy with Confidence},
	Utilisateur = {Guillaume Andrieu},
	Volume = 40,
	Year = 1978}

@article{cavender81,
	Author = {James A. Cavender},
	Journal = {Mathematical Biosciences},
	Pages = {217-229},
	Title = {Tests of Phylogenetic Hypotheses under Generalized Models},
	Utilisateur = {Guillaume Andrieu},
	Volume = 54,
	Year = 1981}

@article{chandon80,
	Author = {Jean Louis Chandon and J. Lemaire and J. Pouget},
	Journal = {R.A.I.R.O. Recherche op{\'e}rationnelle},
	Pages = {157-170},
	Title = {Construction de l'ultram{\'e}trique la plus proche d'une dissimilarit{\'e} au sens des moindres carr{\'e}s},
	Utilisateur = {Gilles Caraux},
	Volume = 14,
	Year = 1980}

@article{chor00,
	Author = {B. Chor and M. Hendy and B. Holland and D. Penny},
	Journal = {Molecular Biology and Evolution},
	Pages = {1529-1541},
	Title = {Multiple maxima of likelihood in phylogenetic trees: an analytic approach},
	Volume = 17,
	Year = 2000}

@article{churchill92,
	Author = {Gary A. Churchill and Arndt von Haesler and William C. Navidi},
	Journal = {Molecular Biology and Evolution},
	Pages = {753-769},
	Title = {Sample size for a phylogenetic inference },
	Utilisateur = {Guillaume Andrieu},
	Volume = 9,
	Year = 1992}

@article{clark92,
	Author = {Andrew G. Clark and Thomas S. Whittam},
	Journal = {Molecular Biology and Evolution},
	Pages = {744-752},
	Title = { Sequencing errors and molecular evolutionary analysis},
	Utilisateur = {Guillaume Andrieu},
	Volume = 9,
	Year = 1992}

@article{clark03,
	Author = { A. Clark and S. Glanowski and R. Nielsen and P. Thomas and A. Kejariwal and M. Todd and D. Tanenbaum and D. Civello and F. Lu and B. Murphy and S. Ferriera and G. Wang and X. Zheng and T. White and J. Sninsky and M. Adams and M. Cargill},
	Journal = {Science},
	Pages = {1960-1963},
	Title = {Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios},
	Volume = 302,
	Year = 2003}

@inproceedings{cohen97,
	Author = {J. Cohen and M. Farach},
	Booktitle = {Proceedings of the 8th Annual ACM-SIAM                    Symposium On Discrete Algorithms},
	Title = {Numerical Taxonomy on Data: Experimental Results},
	Year = 1997}

@article{colless67,
	Author = {Donald H. Colless},
	Journal = {Systematic Zoology},
	Pages = {289-295},
	Title = {The phylogenetic fallacy},
	Utilisateur = {Gilles Caraux},
	Volume = 16,
	Year = 1967}

@article{colonius81,
	Author = {H. Colonius and H.H. Schulze},
	Journal = {British Journal of Math. and Stat. Psychology},
	Pages = {167-180},
	Title = {Tree structures for proximity data},
	Utilisateur = {Vincent},
	Volume = 34,
	Year = 1981}

@article{crandall99,
	Author = {K. Crandall and C. Kelsey and H. Imamichi and H. Lane and N. Salzman},
	Journal = {Molecular Biology and Evolution},
	Pages = {372-382},
	Title = {Parallel evolution of drug resistance in {HIV} : failure of nonsynonymous/synonymous rate ratio to detect selection},
	Volume = 16,
	Year = 1999}

@article{curnow89,
	Author = {R. N. Curnow and T. B. L. Kirkwood},
	Journal = {J. of the Royal Statistical Society},
	Pages = {199-220},
	Title = {Statistical analysis of Desoxyribonucleic Acid Sequence Data-A review},
	Utilisateur = {Guillaume Andrieu},
	Volume = 152,
	Year = 1989}

@incollection{czelusniak90,
	Address = {New York},
	Author = {John Czelusniak and Morris Goodman and Nancy D. Moncrieff and Suzanne M. Kehoe},
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acid sequences},
	Chapter = 37,
	Editor = {Russsell F. Doolittle},
	Note = {{P}resente les meths de branch-swapping sur un arbre},
	Pages = {601-615},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Maximum Parsimony Approach to Construction of Evolutionary Trees from Aligned Homologous Sequences},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@book{darwin,
	Author = {C. Darwin},
	Publisher = {John Murray},
	Title = {On the origin of species},
	Year = 1859}

@article{daubin03,
	Author = {V. Daubin and G. Perri{\`e}re},
	Journal = {Molecular Biology and Evolution},
	Pages = {471-483},
	Title = {{G+C3} structuring along the genome : a common feature in prokaryotes},
	Volume = 20,
	Year = 2003}

@article{day85,
	Author = {W.H. Day and F.R. McMorris},
	Journal = {Bulletin of Math. Biol.},
	Pages = {215-229},
	Title = {A formalization of consensus index methods},
	Volume = 47,
	Year = 1985}

@incollection{day87,
	Author = {W. H. E. Day},
	Booktitle = {Bulletin of Mathematical Biology},
	Pages = {461-467},
	Title = {Computational Complexity of Inferring Phylogenies     from Dissimilarity Matrices},
	Volume = 49,
	Year = 1987}

@incollection{dayhoff78,
	Address = {Washington, D. C.},
	Author = {M. Dayhoff and R. Schwartz and B. Orcutt},
	Booktitle = {Atlas of Protein Sequence and Structure},
	Editor = {M. Dayhoff},
	Pages = {345-352},
	Publisher = {National Biomedical Research Foundation},
	Title = {A model of evolutionary change in proteins},
	Volume = 5,
	Year = 1978}

@incollection{debry92,
	Author = {R. W. DeBry},
	Booktitle = {Molecular Biology and Evolution},
	Pages = {537-551},
	Title = {The Consistency of Several Phylogeny-Inference     Methods under Varying Evolutionary Rates},
	Volume = 9,
	Year = 1992}

@incollection{degens83,
	Address = {Berlin Heidelberg},
	Author = {Paul O. Degens},
	Booktitle = {Numerical Taxonomy},
	Editor = {Joseph Felsenstein},
	Pages = {249-253},
	Publisher = {Springer-Verlag},
	Series = {NATO ASI},
	Title = {Hierarchical cluster methods as maximum likelihood     estimators},
	Utilisateur = {Gilles Caraux},
	Volume = {G1},
	Year = 1983}

@article{delsuc02,
	Author = {F. Delsuc and M. Scally and O. Madsen and M. Stanhope and W. de Jong and F. Catzeflis and M. Springer and E. Douzery},
	Journal = {Molecular Biology and Evolution},
	Pages = {1656-1671},
	Title = {Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting},
	Volume = {19},
	Year = {2002}}

@article{delsuc05,
	Author = {F. Delsuc and H. Brinkmann and H. Philippe},
	Journal = {Nature Review Genetics},
	Pages = {361-375},
	Title = {Phylogenomics and the reconstruction of the tree of life},
	Volume = {6},
	Year = {2005}}

@article{dempster77,
	Author = {A. P. Dempster and N. M. Laird and D. B. Rubin},
	Journal = {J. R. Statist. Soc. B},
	Pages = {1-22},
	Title = {Maximum Likelihood from incomplete data via the \hbox{\it EM} algorithm},
	Utilisateur = {Gilles Caraux et Guillaume Andrieu},
	Volume = 39,
	Year = 1977}

@article{denis02,
	Author = {F. Denis and O. Gascuel},
	Journal = {Discrete Applied Mathematics},
	Title = {On the consistency of the minimum evolution principle of phylogenetic inference},
	Year = 2002}

@article{derchia96,
	Author = {A.M. D'Erchia and C. Gissi and G. Pesole and C. Saccone and U. Arnason},
	Journal = {Nature},
	Pages = {597-600},
	Title = {The guinea-pig is not a rodent},
	Volume = 381,
	Year = 1996}

@article{desoete83,
	Author = {Geert de Soete},
	Commentaire = {Ceci est mon commentaire},
	Journal = {Psychometrika},
	Pages = {621-626},
	Title = {A least squares algorithm for fitting additive trees to proximity data},
	Utilisateur = {Gilles Caraux},
	Volume = 48,
	Year = 1983}

@article{desper02,
	Author = {R. Desper and O. Gascuel},
	Journal = {Journal of Computational Biology},
	Pages = {687-705},
	Title = {Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle},
	Volume = 9,
	Year = 2002}

@article{dickerson71,
	Author = {Richard Dickerson},
	Journal = {Journal of Molecular Evolution},
	Pages = {26-45},
	Title = {The structure of cytochrome $c$ and the rates of molecular evolution},
	Utilisateur = {Gilles Caraux},
	Volume = 1,
	Year = 1971}

@article{dimmic02,
	Author = {M. Dimmic and J. Rest and D. Mindell and D. Goldstein},
	Journal = {Journal of Molecular Evolution},
	Pages = {65-73},
	Title = {{rtREV}: an amino acid substitution matrix for inference of retrovirus and     reverse transcriptase phylogeny},
	Volume = 55,
	Year = 2002}

@incollection{dobson75,
	Address = {Berlin},
	Author = {Annette J. Dobson},
	Booktitle = {Combinatorial Mathematics III},
	Editor = {A. Dold and B. Eckmann},
	Pages = {95-100},
	Publisher = {Springer},
	Series = {Lecture Notes in Mathematics},
	Title = {Comparing the shapes of trees},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Volume = 452,
	Year = 1975}

@incollection{doolittle90,
	Author = {Russel F. Doolittle and Da-Fei Feng},
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acid sequences},
	Chapter = 41,
	Editor = {Russsell F. Doolittle},
	Pages = {659-669},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Nearset Neighbor Procedure for relating Progressively Amino Acid Sequences},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@article{dopazo94,
	Author = {Joaquin Dopazo},
	Journal = {Journal of Molecular Evolution},
	Pages = {300-304},
	Title = {Estimating Errors and Confidence Intervals for     Branch Lengths in Phylogenetic Trees by a Bootstrap Approach},
	Utilisateur = {Guillaume Andrieu},
	Volume = 38,
	Year = 1994}

@article{douady03,
	Author = {C. J. Douady and F. Delsuc and Y. Boucher and W. F. Doolittle and E. J. P. Douzery },
	Journal = {Molecular Biology and Evolution},
	Pages = {248-254},
	Title = {Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability},
	Volume = 20,
	Year = 2003}

@article{douzery03,
	Author = {E. Douzery and F. Delsuc and M. Stanhope and D. Huchon},
	Journal = {Journal of Molecular Evolution},
	Pages = {S201-13},
	Title = {Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations},
	Volume = {57 Suppl 1},
	Year = 2003}


@Article{douzery04,
   Author="Douzery, E. J.  and Snell, E. A.  and Bapteste, E.  and Delsuc, F.  and Philippe, H. ",
   Title="{{T}he timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?}",
   Journal="Proc. Natl. Acad. Sci. U.S.A.",
   Year="2004",
   Volume="101",
   Pages="15386--15391",
   Month="Oct"
}

@article{dress86,
	Author = {A. Dress and A. von Haeseler and M. Krueger},
	Journal = {Studien zur Klassifikation},
	Pages = {299-305},
	Title = {Reconstructing phylogenetic trees using variants of     the "four-point condition"},
	Year = 1986}

@article{drummond03,
	Author = {A. Drummond and O. Pybus and A. Rambaut and R. Forsberg and A. Rodrigo},
	Journal = {Trends in Ecology and Evolution},
	Pages = {481-488},
	Title = {Measurably evolving populations},
	Volume = 18,
	Year = 2003}

@article{drummond06,
	Author = {A. Drummond and S. Ho and M. Phillips and A. Rambaut},
	Journal = {PLoS Biology},
	Pages = {e88},
	Title = {Relaxed phylogenetics and dating with confidence},
	Volume = 4,
	Year = 2006}

@Article{drummond07,
   Author="Drummond, A. J.  and Rambaut, A. ",
   Title="{{B}{E}{A}{S}{T}: {B}ayesian evolutionary analysis by sampling trees}",
   Journal="BMC Evol. Biol.",
   Year="2007",
   Volume="7",
   Pages="214"
}



@article{dudoit02,
	Author = {S. Dudoit and J. Popper Shaffer and J. Boldrick},
	Journal = {U.C. Berkeley Division of Biostatistics Working Paper Series},
	Pages = {http://www.bepress.com/ucbbiostat/paper110},
	Title = {Multiple Hypothesis Testing in Microarray Experiments},
	Year = 2002}


@article{edgar04,
author={R. Edgar},
title={{MUSCLE}: multiple sequence alignment with high accuracy and high throughput},
journal={Nucleic Acids Research},
year={2004},
volume={32},
pages={1792-1797}
}


@article{edwards63,
	Author = {A. W. F. Edwards and L. L. Cavalli-Sforza},
	Journal = {Ann. Hum. Genet.},
	Pages = {104-105},
	Title = {The reconstruction of evolution},
	Volume = 27,
	Year = 1963}

@article{edwards64,
	Author = {A. W. F. Edwards and L. L. Cavalli-Sforza},
	Journal = {Systematics Association Publication.},
	Pages = {67-76},
	Title = {Reconstruction of evolutionary trees},
	Volume = 6,
	Year = 1964}

@book{edwards72,
	Address = {Cambridge, England},
	Author = {A. W. F. Edwards},
	Publisher = {University Press},
	Title = {Likelihood},
	Year = 1972}

@article{efron79,
	Author = {B. Efron},
	Journal = {Ann. Statistics},
	Pages = {1-26},
	Title = {Bootstrap methods: another look at the jackknife},
	Volume = 7,
	Year = 1979}

@article{efron85,
	Author = {B. Efron},
	Journal = {Biometrika},
	Pages = {45-58},
	Title = {Bootstrap confidence intervals for a class of parametric problems},
	Volume = 72,
	Year = 1985}

@article{efron87,
	Author = {Bradley Efron},
	Journal = {Journal of the american statistical association},
	Month = {March},
	Number = 397,
	Pages = {171-185},
	Title = {Better bootstrap confidence intervals},
	Volume = 82,
	Year = 1987}

@book{efron93,
	Author = {Bradley Efron and Robert J. Tibshirani},
	Publisher = {Chapman et Hall},
	Title = {An {I}ntroduction to the {B}ootstrap},
	Utilisateur = {Susan Holmes},
	Year = 1993}

@techreport{efron95,
	Author = {B. Efron and E. Halloran and S. Holmes},
	Institution = {Standford University},
	Number = {Tech. Rep. 179},
	Title = {Bootstrap confidence levels for phylogenetic trees},
	Year = 1995}

@article{efron96,
	Author = {B. Efron and E. Halloran and S. Holmes},
	Journal = {PNAS},
	Pages = {7085-7090},
	Title = {Bootstrap confidence levels for phylogenetic trees},
	Volume = 93,
	Year = 1996}

@article{eigen81,
	Author = {M. Eigen and R. Winkler-Oswatitsch},
	Journal = {Die Naturwissenschaften},
	Pages = {217-228},
	Title = {Transfer-{\sc RNA} : The Early Adaptor},
	Utilisateur = {Guillaume Andrieu},
	Volume = 68,
	Year = 1981}

@article{eigen88,
	Author = {M. Eigen and R. Winkler-Oswatitsch and     A. Dress},
	Journal = {PNAS},
	Pages = {5913-5917},
	Title = {Statistical Geometry in Sequence Space : A Method     of Quantitative Comparative Sequence Analysis },
	Volume = 85,
	Year = 1988}

@incollection{eigen90a,
	Author = {Manfred Eigen and Ruthild Winkler-Oswatitsch},
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acid sequences},
	Chapter = 32,
	Editor = {Russsell F. Doolittle},
	Pages = {505-530},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Statistical Geometry on Sequence Space},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@article{eigen90b,
	Author = {Manfred Eigen and Katja Nieselt-Struwe},
	Journal = {AIDS},
	Pages = {585-593},
	Title = {How old is the Immunodeficiency Virus~?},
	Utilisateur = {Guillaume Andrieu},
	Volume = {4(suppl1)},
	Year = 1990}

@article{elemento02,
	Author = {O. Elemento and O. Gascuel and M.-P. Lefranc },
	Journal = {Molecular Biology and Evolution},
	Pages = {278-288},
	Title = {Reconstructing the duplication history of tandemly repeated genes},
	Volume = {19},
	Year = 2002}

@article{erchia96,
	Author = {A.M. d'Erchia and C. Gissi and G. Pesole and     C. Saccone and U. Arnason},
	Journal = {Nature},
	Pages = {597-600},
	Title = {The guinea-pig is not a rodent},
	Volume = 381,
	Year = 1996}

@article{estabrook72,
	Author = {G.F. Estabrook},
	Journal = {Ann. Rev. Ecol. Syst.},
	Pages = {427-456},
	Title = {Cladistic methodology: a discussion of the theoretical basis                   for the induction of evolutionary history},
	Volume = 3,
	Year = 1972}

@article{estabrook76,
	Author = {G.F. Estabrook and C.S. Johnson and F.R. McMorris},
	Journal = {Mathematical Biosciences},
	Pages = {181-187},
	Title = {A mathematical foundation for the analysis of cladistic                    character compatibility},
	Volume = 29,
	Year = 1976}

@inproceedings{fk96,
	Author = {M. Farach and S. Kannan},
	Booktitle = {Proceedings of the 28th Annual ACM Symposium on the Theory of                   Computing},
	Pages = {230-235},
	Title = {Efficient algorithms for inverting evolution},
	Year = 1996}

@article{farris71,
	Author = {James S. Farris},
	Journal = {Annual Review of Ecology and Systematics},
	Pages = {277-302},
	Title = {The hypothesis of nonspecificity and taxonomic congruence},
	Utilisateur = {Gilles Caraux},
	Volume = 22,
	Year = 1971}

@article{farris73a,
	Author = {James S. Farris},
	Journal = {Systematic Zoology},
	Pages = {250-256},
	Title = {A Probability Model for Inferring Evolutionary Trees},
	Utilisateur = {Guillaume Andrieu},
	Volume = 22,
	Year = 1973}

@article{farris73b,
	Author = {James S. Farris},
	Journal = {American Naturalist},
	Pages = {531-534},
	Title = {Estimation of Amino-Acid Substitution when Back     Mutation can occur},
	Utilisateur = {Guillaume Andrieu},
	Volume = 107,
	Year = 1973}

@article{felsenstein73a,
	Author = {J. Felsenstein},
	Journal = {The American Journal of Human Genetics},
	Pages = {471-492},
	Title = {Maximum-likelihood estimation of evolutionary trees     from continuous characters},
	Utilisateur = {Gilles Caraux},
	Volume = 25,
	Year = 1973}

@article{felsenstein73b,
	Author = {J. Felsenstein},
	Journal = {Systematic Zoology},
	Pages = {240-249},
	Title = {Maximum Likelihood and Minimum Steps Methods for     Estimating Evolutionnary Trees from Data on Discrete     Characters},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Volume = 23,
	Year = 1973}

@article{felsenstein78,
	Author = {J. Felsenstein},
	Journal = {Systematic Zoology},
	Pages = {401-410},
	Title = {Cases in which parsimony and compatibility methods     will be positively misleading},
	Volume = 27,
	Year = 1978}

@article{felsenstein81a,
	Author = {J. Felsenstein},
	Journal = {Journal of Molecular Evolution},
	Pages = {368-376},
	Title = {Evolutionary Trees from {DNA} Sequences: a Maximum Likelihood Approach},
	Volume = 17,
	Year = 1981}

@article{felsenstein81b,
	Author = {J. Felsenstein},
	Journal = {Evolution},
	Note = {({\it construction d'arbrtes par le maximum de vraisemblance})},
	Number = 6,
	Pages = {1229-1242},
	Title = {Evolutionary Trees from gene frequencies and     quantitative characteres : finding maximum     likelihood estimates},
	Volume = 35,
	Year = 1981}

@article{felsenstein83,
	Author = {J. Felsenstein},
	Journal = {J. R. Statist. Soc. A},
	Number = {Part 3},
	Pages = {246-272},
	Title = {Statistical Inference of Phylogenies},
	Volume = 146,
	Year = 1983}

@article{felsenstein84,
	Author = {J. Felsenstein},
	Journal = {Evolution},
	Number = 1,
	Pages = {16-24},
	Title = {Distance methods for inferring phylogenies : a justification},
	Utilisateur = {Gilles Caraux},
	Volume = 38,
	Year = 1984}

@article{felsenstein85a,
	Author = {J. Felsenstein},
	Journal = {Evolution},
	Pages = {783-791},
	Title = {Confidence limits on phylogenies: an     approach using the bootstrap},
	Volume = 39,
	Year = 1985}

@article{felsenstein85b,
	Author = {J. Felsenstein},
	Journal = {Systematic Zoology},
	Pages = {27-33},
	Title = {The number of evolutionary trees},
	Utilisateur = {Gilles Caraux},
	Volume = 34,
	Year = 1985}

@article{felsenstein85c,
	Author = {J. Felsenstein},
	Journal = {Systematic Zoology},
	Number = 2,
	Pages = {152-161},
	Title = {Confidence limits on phylogenies with a molecular clock},
	Utilisateur = {Gilles Caraux},
	Volume = 34,
	Year = 1985}

@article{felsenstein87,
	Author = {J. Felsenstein},
	Journal = {Journal of Molecular Evolution},
	Pages = {123-131},
	Title = { Estimation of Hominoid Phylogeny from a {DNA} Hybridation Data Set},
	Utilisateur = {Guillaume Andrieu},
	Volume = 26,
	Year = 1987}

@article{felsenstein88,
	Author = {J. Felsenstein},
	Journal = {Annual Review of Genetics},
	Pages = {521-565},
	Title = {Phylogenies from molecular sequences:                     inference and reliability},
	Volume = 22,
	Year = 1988}

@book{felsensteinbook,
	Address = {Sunderland, MA},
	Author = {J. Felsenstein},
	Publisher = {Sinauer Associates, Inc.},
	Title = {Inferring phylogenies},
	Year = 2003}

@article{phylip1,
	Author = {J. Felsenstein},
	Journal = {Cladistics},
	Pages = {164-166},
	Title = {Phylogeny Inference Package (Version 3.2)},
	Volume = {5},
	Year = {1989}}

@book{phylip2,
	Address = {Department of Genetics, University of Washington, Seattle},
	Author = {J. Felsenstein},
	Publisher = {Distributed by the author},
	Title = {PHYLIP ({PHYL}ogeny {I}nference {P}ackage) version 3.6a2},
	Year = {1993}}

@article{gaucher01,
	Author = {E. Gaucher and M. Miyamoto and S. Benner},
	Journal = {PNAS},
	Pages = {548-552},
	Title = {Function-structure analysis of proteins using covarion-based evolutionary approaches: {E}longation factors},
	Volume = 98,
	Year = 2001}


@ARTICLE{gouy09,
author = { Manolo Gouy and  Stephane Guindon and  Olivier Gascuel},
title = {Sea{V}iew version 4: {A} multiplatform graphical user interface for sequence
      alignment and phylogenetic tree building.},
journal = {Mol Biol Evol},
year = {2010},
volume = {27},
number = {2},
pages = {221-4}
}

@article{haydon01,
	Author = {D. Haydon and A. Bastos and N. Knowles and A. Samuel},
	Journal = {Genetics},
	Pages = {7-15},
	Title = {Evidence for Positive Selection in Foot-and-Mouth Disease Virus Capsid Genes From Field Isolates},
	Volume = 157,
	Year = 2001}

@article{henikoff92,
	Author = {S. Henikoff and J. Henikoff},
	Journal = {PNAS},
	Pages = {10915-10919},
	Title = {Amino acid substitution matrices from protein blocks.},
	Volume = 89,
	Year = 1992}

@article{hordijk05,
	Author = {W. Hordijk and O. Gascuel},
	Journal = {Bioinformatics},
	Pages = {4338-4347},
	Title = {Improving the efficiency of {SPR} moves in phylogenetic tree search methods based on maximum likelihood.},
	Volume = 21,
	Year = 2005}

@article{huelsenbeck00,
	Author = {J. Huelsenbeck and B. Larget and D. Swofford},
	Journal = {Genetics},
	Pages = {1879-1892},
	Title = {A compound {P}oisson process for relaxing the molecular clock},
	Volume = 154,
	Year = 2000}

@article{kuhner94,
	Author = {M. Kuhner and J. Felsenstein},
	Journal = {Molecular Biology and Evolution},
	Pages = {459-468},
	Title = {A Simulation Comparison of Phylogeny Algorithms     under Equal and Unequal Evolutionary Rates},
	Volume = 11,
	Year = 1994}

@article{felsenstein96,
	Author = {J. Felsenstein and G.A. Churchill},
	Journal = {Molecular Biology and Evolution},
	Pages = {93-104},
	Title = {A Hidden {M}arkov Model approach to variation among sites in rate of evolution},
	Volume = 13,
	Year = 1996}

@incollection{feng90,
	Address = {New-York},
	Author = {Da-Fei Feng and Russel F. Doolittle},
	Booktitle = {Progressive alignement and phylogenetic tree construction of protein sequences},
	Chapter = 23,
	Editor = {Russsell F. Doolittle},
	Pages = {375-387},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Nearset Neighbor Procedure for relating Progressively Amino Acid Sequences},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@article{fitch67,
	Author = {W. M. Fitch and E. Margoliash},
	Journal = {Science},
	Pages = {279-284},
	Title = {Construction of phylogenetic trees},
	Volume = 155,
	Year = 1967}

@article{fitch71,
	Author = {Walter M. Fitch},
	Journal = {Systematic Zoology},
	Title = {Toward defining the course of evolution : minimum     change for a specific tree topology},
	Year = 1971}

@inproceedings{fitch75,
	Author = {W.M. Fitch},
	Booktitle = {Proceedings of the 8th International Conference on Numerical                    Taxonomy},
	Pages = {189-230},
	Title = {Towards finding the tree of Maximum Parsimony},
	Year = 1975}

@article{fitch81,
	Author = {W. M. Fitch},
	Journal = {Journal of Molecular Evolution},
	Pages = {30-37},
	Title = {A non-sequential method for constructing trees and                    hierarchical classifications},
	Volume = 18,
	Year = 1981}

@article{fitchfarris74,
	Author = {Walter M. Fitch and James S. Farris},
	Journal = {Journal of Molecular Evolution},
	Note = {etendent la meth de Fitch71 pr les acides amines,     car il y a pr ce type de data qq ambiguites.},
	Pages = {263-278},
	Title = {Evolutionary trees with minimum nucleotide     replacements form amino acid sequences},
	Utilisateur = {Vincent},
	Volume = 3,
	Year = 1974}

@article{forsberg03,
	Author = {R. Forsberg and F. Christiansen},
	Journal = {Molecular Biology and Evolution},
	Pages = {1252-1259},
	Title = {A codon-based model of host-specific selection in parasites with an application to the {I}nfluenza {A} virus},
	Volume = 20,
	Year = 2003}

@article{foulds84,
	Author = {L.R. Foulds},
	Journal = {Journal of Theoretical  Biology},
	Pages = {471-474},
	Title = {Maximum Savings in the Steiner Problem in Phylogeny},
	Volume = 107,
	Year = 1984}

@article{frommel85,
	Author = {C. Fr\H{o}mmel and H. G. Holzh\H{u}tter},
	Journal = {Journal of Molecular Evolution},
	Pages = {233-257},
	Title = {an estimate on the effect of point mutation and natural  selection on the rate of amino acid replacement in proteins },
	Utilisateur = {Guillaume Andrieu},
	Volume = 21,
	Year = 1985}

@article{fukami89,
	Author = {K. Fukami  and Y. Tateno},
	Journal = {Journal of Molecular Evolution},
	Pages = {460-464},
	Title = {On the maximum likelihood method for estimating molecular trees : uniquesness of the likelihood point},
	Utilisateur = {Gilles Caraux},
	Volume = 28,
	Year = 1989}

@phdthesis{galtierthese,
	Author = {N. Galtier},
	Month = {novembre},
	School = {Universit{\'e} Claude Bernard - Lyon I},
	Title = {L'approche statistique en phylog{\'e}nie mol{\'e}culaire~: influence des composition en bases variables},
	Year = 1997}

@article{galtier01,
	Author = {N. Galtier},
	Journal = {Molecular Biology and Evolution},
	Pages = {866-873},
	Title = {Maximum-likelihood phylogenetic analysis under a covarion-like model},
	Volume = 18,
	Year = 2001}

@article{galtier99,
	Author = {N. Galtier and N. Tourasse and M. Gouy},
	Journal = {Science},
	Pages = {220-221},
	Title = {A nonhyperthermophilic common ancestor to extant life forms},
	Volume = 283,
	Year = 1999}

@article{galtier98,
	Author = {N. Galtier and M. Gouy},
	Journal = {Molecular Biology and Evolution},
	Pages = {871-879},
	Title = {Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of {DNA} sequence evolution for phylogenetic analysis},
	Volume = 15,
	Year = 1998}

@article{galtier95,
	Author = {N. Galtier and M. Gouy},
	Journal = {PNAS},
	Pages = {11317-11321},
	Title = {Inferring phylogenies from {DNA} sequences of unequal base compositions},
	Volume = 92,
	Year = 1995}

@article{galtier04,
	Author = {N. Galtier and A. Jean-Marie},
	Journal = {Journal of Computational Biology},
	Pages = {727-733},
	Title = {Markov-modulated {M}arkov chains and the covarion process of molecular evolution},
	Volume = 11,
	Year = 2004}

@book{gamerman06,
	Author = {Dani Gamerman and Hedibert F. Lopes },
	Isbn = {1584885874},
	Publisher = {Chapman and Hall/CRC},
	Title = {Markov Chain Monte Carlo: Stochastic Simulation for Bayesian Inference},
	Year = {2006}}

@book{gareyjohnson,
	Address = {San Fransisco},
	Author = {M. Garey and D. Johnson},
	Publisher = {Freeman},
	Title = {{C}omputers and {I}ntractability - {A} guide to the     {T}heory of {NP}-{C}ompleteness},
	Year = 1979}

@article{gascuel92,
	Author = {O. Gascuel and G. Caraux},
	Journal = {Pattern Recognition letters},
	Note = {({\it Estimation d'une probab {\`a} partir d'une fr{\'e}quence}) },
	Pages = {757-764},
	Title = {{D}istribution-free performance bounds with the     resubstitution error estimate},
	Volume = {13},
	Year = {1992}}

@article{gascuel94,
	Author = {O. Gascuel},
	Journal = {Molecular Biology and Evolution},
	Pages = {961-963},
	Title = {A Note on {S}attah and {T}versky's, {S}aitou and {N}ei's,     and {S}tudier and {K}eppler's Algorithms for Inferring     Phylogenies from Evolutionary Distances},
	Volume = {11},
	Year = {1994}}

@article{gascuel96,
	Author = {O. Gascuel and D. Levy},
	Journal = {J. of Classification},
	Title = {A reduction for approximating a (non-metric)     dissimilarity by a tree distance},
	Year = 1996}

@article{gascuelNJ,
	Author = {O. Gascuel},
	Journal = {Molecular Biology and Evolution},
	Pages = {685-695},
	Title = {{B}IO{NJ}: an Improved Version of the {NJ} Algorithm Based on a Simple Model of Sequence Data},
	Volume = {14},
	Year = 1997}

@article{gascuel00,
	Author = {O. Gascuel},
	Journal = {Molecular Biology and Evolution},
	Pages = {401-405},
	Title = {On the optimization principle in phylogenetic analysis and the minimum-evolution criterion},
	Volume = 17,
	Year = 2000}

@article{gascuel01,
	Author = {O. Gascuel and D. Bryant and F. Denis},
	Journal = {Systematic Biology},
	Pages = {621-627},
	Title = {Strengths and limitations of the minimum evolution principle},
	Volume = {50},
	Year = 2001}

@article{gascuel03,
	Author = {O. Gascuel and M. Hendy and A. Jean-Marie and R. McLachlan},
	Journal = {Systematic Biology},
	Pages = {110-118},
	Title = {The combinatorics of tandem duplication trees},
	Volume = {52},
	Year = {2003}}

@incollection{gascuel97,
	Address = {Providence, USA},
	Author = {O. Gascuel},
	Booktitle = {Mathematical Hierarchies and Biology},
	Editor = {B. Mirkin and F.R. McMorris and F.S. Roberts and     A. Rzhetsky},
	Pages = {149-170},
	Publisher = {Am. Math. Society},
	Title = {Concerning the {NJ} algorithm and its unweighted     version {UNJ}},
	Year = 1997}

@incollection{gascuel05,
	Address = {Oxford},
	Author = {O. Gascuel and D. Bertrand and O. Elemento},
	Booktitle = {Mathematics of evolution and phylogeny},
	Editor = {O. Gascuel},
	Pages = {205-235},
	Publisher = {Clarendon press},
	Title = {Reconstructing the duplication history of tandemly repeated sequences},
	Year = 2005}

@Article{gaut92,
   Author="Gaut, B. S.  and Muse, S. V.  and Clark, W. D.  and Clegg, M. T. ",
   Title="{{R}elative rates of nucleotide substitution at the rbc{L} locus of monocotyledonous plants}",
   Journal="Journal of Molecular Evolution",
   Year="1992",
   Volume="35",
   Pages="292--303",
   Month="Oct"
}

@article{gaut95,
	Author = {B.S. Gaut and P.O. Lewis},
	Journal = {Molecular Biology and Evolution},
	Pages = {152-162},
	Title = {Success of maximum likelihood phylogeny inference in the four-taxon case},
	Volume = 12,
	Year = 1995}

@book{gill81,
	Address = {London},
	Author = {P. Gill and W. Murray and M. Wright},
	Publisher = {Academic Press},
	Title = {Practical optimization},
	Year = 1981}

@article{geman84,
        author = {Geman, Stuart   and Geman, Donald},
	journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	keywords = {annealing, mrf, simulated},
	month = {November},
	number = {6},
	pages = {721--741},
	posted-at = {2008-05-07 06:09:28},
	priority = {2},
	publisher = {Routledge},
	title = {Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images},
	volume = {6},
	year = {1984}
}

@dea{giordano91,
	Address = {Montpellier},
	Author = {Jean-Yves Giordano},
	School = {Universit{\'e} Montpellier II},
	Title = {{R}epr{\'e}sentation arbor{\'e}e des {P}roximit{\'e}s et {A}rbres  {P}hyllog{\'e}n{\'e}tique},
	Utilisateur = {Guillaume Andrieu},
	Year = 1991}

@article{gojobori82,
	Author = {Takashi Gojobori and Kazushige Ishii and Masatoshi Nei},
	Journal = {Journal of Molecular Evolution},
	Pages = {414-423},
	Title = {Estimation of Average Number of Nucleotide Substitutions when the Rate of Substitution varies with Nucleotide},
	Utilisateur = {Guillaume Andrieu},
	Volume = 18,
	Year = 1982}

@incollection{gojobori90,
	Author = {Takashi Gojobori and Etsuko N. Moriyama and M. Kimura},
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acid sequences},
	Chapter = 33,
	Editor = {Russsell F. Doolittle},
	Pages = {531-550},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Statistical Methods for Estimating Sequence Divergence},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@article{golding83,
	Author = {G. B. Golding},
	Journal = {Molecular Biology and Evolution},
	Pages = {125-142},
	Title = {Estimates of {DNA} and protein sequence divergence: an examination of some assumptions},
	Volume = 1,
	Year = 1983}

@article{goldman93,
	Author = {N. Goldman },
	Journal = {Journal of Molecular Evolution},
	Pages = {182-198},
	Title = {Statistical tests of models of {DNA} substitution},
	Volume = 36,
	Year = 1993}

@article{goldman94,
	Author = {N. Goldman and Z. Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {725-736},
	Title = {A Codon-based model of nucleotide substitution for protein-coding {DNA} sequences},
	Volume = 11,
	Year = 1994}

@article{goldman98a,
	Author = {N. Goldman},
	Journal = {Proceedings of the  Royal Society B: Biological Sciences},
	Pages = {1779-1786},
	Title = {Phylogenetic information and experimental design in molecular systematics },
	Volume = 265,
	Year = 1998}

@article{goldman98b,
	Author = {N. Goldman and J. Thorne and D. Jones},
	Journal = {Genetics},
	Pages = {445-458},
	Title = {Assessing the impact of secondary structure and solvent accessibility on protein evolution},
	Volume = 149,
	Year = 1998}

@article{goldman00,
	Author = {N. Goldman and S. Whelan},
	Journal = {Molecular Biology and Evolution},
	Pages = {975-978},
	Title = {Statistical tests of {G}amma-distributed rate heterogeneity in models of sequence evolution in phylogenetics},
	Volume = 17,
	Year = 2000}

@article{goodman65,
	Author = {Leo A. Goodman},
	Journal = {Technometrics},
	Month = {MAY},
	Number = 2,
	Pages = {247-253},
	Title = {On Simultaneous Confidence Intervals for     Multinomial Proportions },
	Volume = 7,
	Year = 1965}

@article{gouy84,
	Author = {M. Gouy and F. Milleret and C. Mugnier and M. Jacobzone and C. Gautier},
	Journal = {Nucleic Acids Research},
	Number = 2,
	Pages = {121-127},
	Title = {{ACNUC}: a nucleic acid sequence data base and analysis system},
	Volume = 12,
	Year = 1984}

@article{graur91,
	Author = {D. Graur and W.A. Hide and W.-H. Li},
	Journal = {Nature},
	Pages = {649-652},
	Title = {Is the guinea-pig a rodent?},
	Volume = 351,
	Year = 1991}

@article{gu95,
	Author = {X. Gu and Y.X. Fu and W.H. Li},
	Journal = {Molecular Biology and Evolution},
	Pages = {546-557},
	Title = {Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites},
	Volume = 12,
	Year = 1995}

@article{gu97,
	Author = {X. Gu and J.D. Zhang},
	Journal = {Molecular Biology and Evolution},
	Pages = {1106-13},
	Title = {A simple method for estimating the parameter of substitution rate variation among sites},
	Volume = 14,
	Year = 1997}

@article{gu98,
	Author = {X. Gu and W.H. Li},
	Journal = {PNAS},
	Pages = {5899-5905},
	Title = {Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution},
	Volume = 95,
	Year = 1998}

@inproceedings{guenoche00,
	Author = {Alain Gu{\'e}noche},
	Booktitle = {Recueil des Actes JOBIM 2000},
	Editor = {O. Gascuel and M.-F Sagot},
	Pages = {181-191},
	Title = {Quelle confiance accorder {\`a} une repr{\'e}sentation arbor{\'e}e ?},
	Year = 2000}

@article{guenoche87,
	Author = {Alain Guenoche},
	Journal = {Math. Sci. hum.},
	Pages = {21-40},
	Title = {Cinq algorithmes d'approximation d'une dissimilarit{\'e} par  des arbres {\`a} distances additives},
	Utilisateur = {Gilles Caraux and Denise Levy},
	Volume = 98,
	Year = 1987}

@inproceedings{guenoche00b,
	Author = {A. Gu{\'e}noche and H. Garreta},
	Booktitle = {Computational biology, LNCS 2066},
	Pages = {45-46},
	Title = {Can we have confidence in a tree representation ?},
	Year = 2000}

@book{gilks95,
	author = {W. R. Gilks and S. Richardson and D. Spiegelhalter},
	publisher = {{Chapman \& Hall/CRC}},
	title = {Markov Chain Monte Carlo in Practice},
	year = {1995}
}


@article{gray09,
author="R. Gray and A. Drummond and Greenhill S.",
title="Language phylogenies reveal expansion pulses and pauses in {P}acific settlement",
journal="Science",
year="2009",
pages={479-483}
}


@article{guindon01,
	Author = {S. Guindon and G. Perri{\`e}re},
	Journal = {Molecular Biology and Evolution},
	Pages = {1838-40},
	Title = {Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes},
	Volume = 18,
	Year = 2001}

@article{guindon02,
	Author = {S. Guindon and O. Gascuel},
	Journal = {Molecular Biology and Evolution},
	Pages = {534-543},
	Title = {Efficient biased estimation of evolutionary distances when substitution rates vary across sites},
	Volume = 19,
	Year = 2002}

@article{guindon03,
	Author = {S. Guindon and O. Gascuel},
	Journal = {Systematic Biology},
	Pages = {696-704},
	Title = {A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood},
	Volume = 52,
	Year = 2003}

@article{guindon04,
	Author = {S. Guindon and A. Rodrigo and K. Dyer and J. Huelsenbeck},
	Journal = {PNAS},
	Pages = {12957-12962},
	Title = {Modeling the site-specific variation of selection patterns along lineages},
	Volume = {101},
	Year = 2004}

@article{guindon05,
	Author = {S. Guindon and F. Lethiec and P. Duroux and O. Gascuel},
	Journal = {Nucleic Acids Research},
	Pages = {557-559},
	Title = {{PHYML} {O}nline -- a web server for fast maximum likelihood-based phylogenetic inference},
	Volume = {33(Web Server issue)},
	Year = 2005}

@article{guindon06,
	Author = {S. Guindon and M. Black and A. Rodrigo},
	Journal = {Molecular Biology and Evolution},
	Pages = {919-926},
	Title = {Control of the False Discovery Rate Applied to the Detection of Positively Selected Amino Acid Sites.},
	Volume = {23},
	Year = 2006}

@article{gusfield91,
	Author = {D. Gusfield},
	Journal = {Networks},
	Pages = {19-28},
	Title = {Efficient Algorithms for inferring evolutionnary trees},
	Volume = 21,
	Year = 1991}

@article{hamming,
	Author = {R. W. Hamming},
	Journal = {The Bell System Technical Journal},
	Number = 2,
	Pages = {147-160},
	Title = {Error Detecting and Error Correcting Codes},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu },
	Volume = 26,
	Year = 1950}

@article{harshman94,
	Author = {J. Harshman},
	Journal = {Systematic Biology},
	Number = 3,
	Pages = {419-424},
	Title = {The effect of irrelevant characters on bootstrap values},
	Utilisateur = {Vincent},
	Volume = 43,
	Year = 1994}

@article{hartigan72,
	Author = {J. Hartigan},
	Journal = {Biometrics},
	Pages = {53-65},
	Title = {Minimum mutation fits to a given tree},
	Volume = 29,
	Year = 1972}

@article{hasegawa85,
	Author = {M. Hasegawa and H. Kishino and T. Yano},
	Journal = {Journal of Molecular Evolution},
	Pages = {160-174},
	Title = {Dating of the {H}uman-{A}pe Splitting by a Molecular Clock of Mitochondrial-{DNA}},
	Utilisateur = {Guillaume Andrieu},
	Volume = 22,
	Year = 1985}

@article{hasegawa87,
	Author = {M. Hasegawa and H. Kishino and T. Yano},
	Journal = {Journal of Molecular Evolution},
	Pages = {132-147},
	Title = {Man's Place in Hominoidea as Inferred from Molecular Clocks of {DNA}},
	Utilisateur = {Guillaume Andrieu},
	Volume = 26,
	Year = 1987}

@article{hasegawa89,
	Author = {H. Kishino and M. Hasegawa},
	Journal = {Journal of Molecular Evolution},
	Pages = {170-179},
	Title = {Evaluation of the maximum likelihood estimate of the evolutionnary tree topology from {DNA} sequence data, and the branching order in Homonoidea},
	Volume = 29,
	Year = 1989}

@article{hasegawa94,
	Author = {M. Hasegawa and H. Kishino},
	Journal = {Molecular Biology and Evolution},
	Pages = {142-145},
	Title = {Accuracies of the Simple Methods for Estimating the     Bootstrap Probability of a Maximum-Likelihood Tree},
	Volume = 11,
	Year = 1994}

@article{hein89,
	Author = {J. Hein},
	Journal = {Molecular Biology and Evolution},
	Pages = {669-684},
	Title = {A tree reconstruction method that is economical in     the number of pairwise comparisons used.},
	Utilisateur = {Vincent},
	Volume = 6,
	Year = 1989}

@incollection{hein90,
	Author = {J. Hein},
	Booktitle = {Molecular evolution : computer analysis of     protein and nucleic acid sequences},
	Chapter = 39,
	Editor = {Russsell F. Doolittle},
	Pages = {626-644},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Unified Approach to Alignement and Phylogenies},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@article{hein93,
	Author = {Jotun Hein },
	Journal = {Journal of Molecular Evolution},
	Pages = {396-405},
	Title = {a heuristic method to reconstruct the history  of sequences subject to recombinaison},
	Utilisateur = {G. Andrieu},
	Volume = 36,
	Year = 1993}

@incollection{hendy82,
	Author = {M.D. Hendy and D. Penny},
	Booktitle = {Mathematical Biosciences},
	Pages = {277-290},
	Publisher = {Elsevier Science Publishing},
	Title = {Branch and bound Algorithms to Determine Minimal     Evolutionary Trees},
	Utilisateur = {Vincent},
	Volume = 59,
	Year = 1982}

@article{hendy89,
	Author = {M.D. Hendy and D. Penny},
	Journal = {Syst Zool},
	Number = 4,
	Pages = {297-309},
	Title = {A framework for the quantitative study of     evolutionary trees},
	Utilisateur = {Vincent},
	Volume = 38,
	Year = 1989}

@article{hendy93,
	Author = {M.D. Hendy and D. Penny},
	Journal = {Journal of Classification},
	Pages = {297-309},
	Title = {Spectral analysis of phylogenetic data},
	Volume = 10,
	Year = 1993}

@article{hendy94,
	Author = {M. Hendy and D. Penny and M. A. Steel},
	Journal = {PNAS},
	Pages = {3339-3343},
	Title = {A discrete {F}ourier analysis for evolutionary trees},
	Volume = 91,
	Year = 1994}

@article{hg01,
	Author = {{International Human Genome Sequencing Consortium}},
	Journal = {Nature},
	Pages = {860-921},
	Title = {Initial sequencing and analysis of the human genome},
	Volume = 409,
	Year = 2001}

@incollection{higgins96,
	Address = {San Diego},
	Author = {D. G. Higgins and J. D. Thompson and J. T. Gibbson},
	Booktitle = {Methods in enzymology},
	Editor = {R. F. Doolittle},
	Pages = {383-401},
	Publisher = {Academic Press},
	Title = {Using {CLUSTAL} for multiple sequence alignments},
	Year = 1996}

@inbook{hiv_epitope,
	Address = {Los Alamos, New Mexico},
	Author = {B. Korber and C. Brander and B. Haynes and R. Koup and C. Kuiken and J. Moore and B. Walker and D. Watkins},
	Publisher = {Los Alamos National Laboratory, Theoretical Biology and Biophysics},
	Title = {{HIV} molecular immunology database 2002},
	Year = 2002}

@inbook{karlin,
	Address = {New York},
	Author = {Samuel Karlin},
	Chapter = { No VII Examples of continuous Time {M}arkov Chains },
	Pages = {189-209},
	Publisher = {Academic Press},
	Title = {A first course in Stochastic processes},
	Utilisateur = {Guillaume Andrieu},
	Year = 19}

@article{koshi96,
	Author = {J. Koshi and R. Goldstein},
	Journal = {Journal of Molecular Evolution},
	Pages = {313-320},
	Title = {Probabilistic reconstruction of ancestral protein sequences},
	Volume = 42,
	Year = 1996}

@article{koshi98,
	Author = {J. Koshi and R. Goldstein},
	Journal = {Proteins},
	Pages = {289-295},
	Title = {Models of natural mutations including site heterogeneity},
	Volume = 32,
	Year = 1998}

@article{kirkpatrick83,
	Author = {S. Kirkpatrick and C. D. Gelatt and M. P. Vecchi},
	Journal = {Science},
	Pages = {671-680},
	Title = {Optimization by simulated annealing},
	Volume = 220,
	Year = 1983}

@inbook{hillis91,
	Author = {D.M. Hillis},
	Chapter = 13,
	Note = {Preliminsaire a l'article hilhuels92},
	Pages = {278-294},
	Title = {Discriminating Between Phylogenetic Signal and     Random Noise in {DNA} Sequences},
	Utilisateur = {Vincent}}

@article{hillishuels92,
	Author = {D.M. Hillis and J.P. Huelsenbeck},
	Journal = {Journal of Heredity},
	Note = {Examine la distribution des arbres les plus     parcimonieux : gaussienne applatie},
	Pages = {189-195},
	Title = {Signal, Noise, and Reliability in Molecular     Phylogenetic Analyses},
	Volume = 83,
	Year = 1992}

@article{ho05,
	Author = {S. Ho and M. Phillips and A. Drummond and A. Cooper},
	Journal = {Molecular Biology and Evolution},
	Pages = {1355-1363},
	Title = {Accuracy of rate estimation using relaxed-clock models with a critical focus on the early {M}etazoan radiation},
	Volume = 22,
	Year = 2005}

@article{holm79,
	Author = {S. Holm},
	Journal = {Scandinavian Journal of Statistics},
	Pages = {65-70},
	Title = {A simple sequentially rejective multiple test procedure},
	Volume = 6,
	Year = 1979}

@article{holmquist72a,
	Author = {Richard Holmquist},
	Journal = {Journal of Molecular Evolution},
	Pages = {115-133},
	Title = {Theoretical foundations for a quantitative approach to paleogenetics {Part I : DNA}},
	Utilisateur = {Gilles Caraux et Guillaume Andrieu},
	Volume = 1,
	Year = 1972}

@article{holmquist72b,
	Author = {Richard Holmquist},
	Journal = {Journal of Molecular Evolution},
	Pages = {211-222},
	Title = {Empirical support for stochastic model of evolution},
	Utilisateur = {Gilles Caraux et Guillaume Andrieu},
	Volume = 1,
	Year = 1972}

@article{holmquist83,
	Author = {R. Holmquist and M. Goodman and T. Conroy and J. Czelusniak},
	Journal = {Journal of Molecular Evolution},
	Pages = {437-448},
	Title = {The spatial distribution of fixed mutations within genes coding for proteins},
	Volume = 19,
	Year = 1983}

@article{huelsenbeck93,
	Author = {J. P. Huelsenbeck and D. Hillis},
	Journal = {Systematic Biology},
	Pages = {247-264},
	Title = {Success of phylogenetic methods in the four-taxon case},
	Volume = 42,
	Year = 1993}

@article{huelsenbeck95a,
	Author = {J. P. Huelsenbeck},
	Journal = {Systematic Biology},
	Pages = {17-48},
	Title = {Performance of phylogenetic methods in simulation},
	Volume = 44,
	Year = 1995}

@article{huelsenbeck95b,
	Author = {J. P. Huelsenbeck},
	Journal = {Molecular Biology and Evolution},
	Pages = {843-849},
	Title = {The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining},
	Volume = 12,
	Year = 1995}

@article{huelsenbeck97a,
	Author = {J. P. Huelsenbeck and K. A. Crandall},
	Journal = {Annual Review of Ecology and Systematics},
	Pages = {437-466},
	Title = {Phylogeny estimation and hypothesis testing using maximum likelihood},
	Volume = 28,
	Year = 1997}

@article{huelsenbeck97b,
	Author = {J. Huelsenbeck and B. Rannala},
	Journal = {Science},
	Pages = {218-219},
	Title = {Phylogenetic methods come of age: testing hypotheses in an evolutionary context},
	Volume = 276,
	Year = 1997}

@article{huelsenbeck99,
	Author = {J. Huelsenbeck and R. Nielsen},
	Journal = {Journal of Molecular Evolution},
	Pages = {86-93},
	Title = {Variation in the pattern of nucleotide substitution across sites},
	Volume = 48,
	Year = 1999}

@article{huelsenbeck01,
	Author = {J. Huelsenbeck and F. Ronquist},
	Journal = {Bioinformatics},
	Pages = {754-755},
	Title = {{MRBAYES} : Bayesian inference of phylogenetic trees},
	Volume = 17,
	Year = 2001}

@article{huelsenbeck01a,
	Author = {J. P. Huelsenbeck and F. Ronquist and R. Nielsen and J. P. Bollack},
	Journal = {Science},
	Pages = {2310-2314},
	Title = {Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology},
	Volume = 294,
	Year = 2001}

@article{huelsenbeck01c,
	Author = {J. P. Huelsenbeck and J. P. Bollback},
	Journal = {Systematic Biology},
	Pages = {351-366},
	Title = {Empirical and hierarchical bayesian estimation of ancestral states},
	Volume = 50,
	Year = 2001}

@article{huelsenbeck02,
	Author = {J. P. Huelsenbeck},
	Journal = {Molecular Biology and Evolution},
	Pages = {698-707},
	Title = {Testing a Covariotide Model of {DNA} Substitution},
	Volume = 19,
	Year = 2002}

@article{huelsenbeck04,
	Author = {J. Huelsenbeck and B. Larget and M. Alfaro},
	Journal = {Molecular Biology and Evolution},
	Pages = {1123-1133},
	Title = {Bayesian phylogenetic model selection using reversible jump markov chain monte carlo.},
	Volume = 21,
	Year = 2004}

@article{huelsenbeck04b,
	Author = {J. Huelsenbeck and K. Dyer},
	Journal = {Journal of Molecular Evolution},
	Pages = {661-672},
	Title = {Bayesian estimation of positively selected sites},
	Volume = 58,
	Year = 2004}

@article{huelsenbeck06,
	Author = {J. Huelsenbeck and S. Jain and S. Frost and S. Pond},
	Journal = {PNAS},
	Pages = {6263-6268},
	Title = {A Dirichlet process model for detecting positive selection in protein-coding {DNA} sequences},
	Volume = 103,
	Year = 2006}




@article{hughes88,
	Author = {A. Hughes and M. Nei},
	Journal = {Nature},
	Pages = {167-170},
	Title = {Pattern of nucleotide substitution at major histocompatibility complex class {I} loci reveals overdominant selection},
	Volume = 335,
	Year = 1988}

@article{hughes90,
	Author = {A. Hughes and T. Ota and M. Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {515-524},
	Title = {Positive darwinian selection promotes charge profile diversity in the antigen-binding cleft of class {I} major-histocompatibility-complex molecules},
	Volume = 7,
	Year = 1990}

@article{mrbayes,
	Author = {J. P. Huelsenbeck and F. Ronquist},
	Journal = {Bioinformatics},
	Pages = {754-755},
	Title = {{M}r{B}ayes: {B}ayesian inference of phylogeny},
	Volume = 17,
	Year = 2001}

@article{irwin91,
	Author = {David M. Irwin and Thomas D. Kocher and Allan C. Wilson},
	Journal = {Journal of Molecular Evolution},
	Pages = {128-144},
	Title = {{E}volution of the {C}ytochrome {\em b} {G}ene of {M}amals},
	Utilisateur = {F.Catzeflis et G. Andrieu},
	Volume = 32,
	Year = 1991}

@techreport{jiang92,
	Author = {T. Jiang and Ming Li},
	Institution = {Mc Master Univ. and University of Waterloo},
	Title = {Some optimizations problems related to molecular biology},
	Year = 1992}

@article{jiang94,
	Author = {Tao Jiang, Eugene L. Lawler, Lusheng Wang},
	Title = {Aligning Sequences via an Evolutionary Tree:     Complexity and Approximation},
	Year = 1994}

@article{jin90,
	Author = {L. Jin and M. Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {82-102},
	Title = {Limitations of the evolutionary parsimony method of phylogenetic analysis},
	Volume = 7,
	Year = 1990}

@article{jin94,
	Author = {Li Jin and Ranajit Chakraborty},
	Journal = {Molecular Biology and Evolution},
	Pages = {120-127},
	Title = {Estimation of genetic distance and coefficient of gene diversity from single-probe multilocus {DNA} fingerprinting data},
	Utilisateur = {Gilles Caraux},
	Volume = 11,
	Year = 1994}

@incollection{johnson90,
	Address = {New York},
	Author = {Mark S. Johnson and Andrej Sali and Tom L. Blundell},
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acid sequences},
	Chapter = 42,
	Editor = {Russsell F. Doolittle},
	Pages = {670-690},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Phylogenetic Relationships from Three-Dimensional Protein Structures},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@article{jones92,
	Author = {D. Jones and W. Taylor and J. Thornton},
	Journal = {Computer Applications in the Biosciences (CABIOS)},
	Pages = {275-282},
	Title = {The rapid generation of mutation data matrices from protein sequences},
	Volume = 8,
	Year = 1992}

@incollection{jukes69,
	Address = {New York},
	Author = {T. Jukes and C. Cantor},
	Booktitle = {Mammalian Protein Metabolism},
	Chapter = {24},
	Editor = {H. Munro},
	Pages = {21-132},
	Publisher = {Academic Press},
	Title = {Evolution of protein molecules},
	Utilisateur = {Gilles Caraux},
	Volume = {III},
	Year = 1969}

@Manual{R,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2013},
    url = {http://www.R-project.org/},
  }

@article{kaj03,
  title={The coalescent process in a population with stochastically varying size},
  author={Kaj, Ingemar and Krone, Stephen M},
  journal={Journal of Applied Probability},
  Volume = 40,
  pages={33--48},
  year={2003},
  publisher={JSTOR}
}


@article{kannan95,
	Author = {S. Kannan and T. Warnow},
	Journal = {SIAM J. Comp.},
	Number = 3,
	Pages = {511-519},
	Title = {Tree reconstruction from partial orders},
	Volume = 24,
	Year = 1995}

@article{kannan97,
	Author = {S. Kannan},
	Journal = {Journal of the indian institute of science},
	Number = 4,
	Pages = {353-364},
	Title = {consensus of trees : desirable properties and computationnal methods},
	Volume = 77,
	Year = 1997}

@article{kaplan79,
	Author = {N. Kaplan and C.H. Langley},
	Journal = {Journal of Molecular Evolution},
	Pages = {295-304},
	Title = {A new estimate of sequence divergence of mitochondrial                     {\sc DNA} Using restriction endonuclease mappings},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Volume = 13,
	Year = 1979}

@inbook{karlin,
	Address = {New York},
	Author = {Samuel Karlin},
	Chapter = { No VII Examples of continuous Time {M}arkov Chains },
	Pages = {189-209},
	Publisher = {Academic Press},
	Title = {A first course in Stochastic processes},
	Utilisateur = {Guillaume Andrieu},
	Year = 19}

@article{karlin93,
	Author = {Samuel Karlin and Stephen F. Altschul},
	Journal = {PNAS},
	Pages = {5873-5877},
	Title = {Applications and Statistics for multiple     hight-scoring segments in molecular Sequences},
	Utilisateur = {Guillaume Andrieu},
	Volume = 90,
	Year = 1993}

@article{kashyap74,
	Author = {R. L. Kashyap and S. Subas},
	Journal = {Journal of Theoretical Biology},
	Pages = {75-101},
	Title = {Statistical estimation of parameters in a     phylogenetic tree using a dynamic model of the     substitutional process},
	Utilisateur = {Gilles Caraux},
	Volume = 47,
	Year = 1974}

@article{kaslow87,
	Author = {R. Kaslow and D. Ostrow and R. Detel and J. Phair and B. Polk and C. Rinaldo},
	Journal = {American Journal of Epidemiology},
	Pages = {310-318},
	Title = {The {M}ulticenter {AIDS} {C}ohort {S}tudy : rationale, organization, and selected characteristics of the participants},
	Volume = 126,
	Year = 1987}

@book{kendall73,
	Address = {London},
	Author = {M. G. Kendall and A. Stuart},
	Publisher = {Griffin},
	Title = {The Advanced Theory of Statistics},
	Volume = {II~: Inference and relationship},
	Year = 1973}

@article{kidd71,
	Author = {K.K. Kidd and L.A. Sgaramella-Zonta},
	Journal = {The American Journal of Human Genetics},
	Pages = {235-252},
	Title = {Phylogenetic analysis: concepts and methods},
	Volume = 23,
	Year = 1971}

@article{kimura72,
	Author = {M. Kimura and Tomoko Otha},
	Journal = {Journal of Molecular Evolution},
	Pages = {87-90},
	Title = { On the stochastic model for estimation of     mutational distance between homologous proteins},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Volume = 2,
	Year = 1972}

@article{kimura80,
	Author = {M. Kimura},
	Journal = {Journal of Molecular Evolution},
	Pages = {111-120},
	Title = {A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences},
	Utilisateur = {Guillaume Andrieu},
	Volume = 16,
	Year = 1980}

@article{kimura81,
	Author = {M. Kimura},
	Journal = {PNAS},
	Pages = {454-458},
	Title = {Estimation of evolutionary distances between homologous nucleotide sequences},
	Volume = 78,
	Year = 1981}

@article{kimura87,
	Author = {M. Kimura},
	Journal = {Journal of Molecular Evolution},
	Pages = {24-33},
	Title = {Molecular Evolutionnary Clock and the Neutral Theory},
	Utilisateur = {Guillaume Andrieu},
	Volume = 26,
	Year = 1987}

@article{kingman82,
	Author = {Kingman, J. F. C. },
	Citeulike-Article-Id = {3431666},
	Journal = {Stochastic Processes and their Applications},
	Keywords = {coalescent, ebsp-paper},
	Pages = {235--248},
	Posted-At = {2008-10-20 21:06:45},
	Priority = {0},
	Title = {The coalescent},
	Volume = {13},
	Year = {1982}}

@article{kishino89,
	Author = {H. Kishino and  M. Hasegawa},
	Journal = {Journal of Molecular Evolution},
	Pages = {170-179},
	Title = {Evaluation of the Maximum Likelihood Estimate of the Evolutionnary Tree Topology from {DNA} Sequence Data, and the Branching Order in Hominoidea},
	Utilisateur = {Gilles Caraux and  Guillaume Andrieu},
	Volume = 29,
	Year = 1989}

@incollection{kishino90,
	Address = {New York},
	Author = {H. Kishino and M. Hasegawa },
	Booktitle = {Molecular evolution : computer analysis of                       protein and nucleic acid sequences},
	Chapter = 34,
	Editor = {Russsell F. Doolittle},
	Pages = {550-570},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Converting Distance to Time : Application to Human                     Evolution},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@article{kishino90b,
	Author = {H. Kishino and T. Miyata and M. Hasegawa},
	Journal = {Journal of Molecular Evolution},
	Pages = {151-160},
	Title = {Maximum likelihood inference of protein phylogeny and the origin of chloroplasts},
	Volume = 31,
	Year = 1990}

@Article{kishino01,
   Author="Kishino, H.  and Thorne, J.  and Bruno, W.",
   Title="{{P}erformance of a divergence time estimation method under a probabilistic model of rate evolution}",
   Journal="Molecular Biology and Evolution",
   Year="2001",
   Volume="18",
   Pages="352--361",
   Month="Mar"
}

@Article{kitazoe07,
   Author="Kitazoe, Y.  and Kishino, H.  and Waddell, P. J.  and Nakajima, N.  and Okabayashi, T.  and Watabe, T.  and Okuhara, Y. ",
   Title="{{R}obust time estimation reconciles views of the antiquity of placental mammals}",
   Journal="PLoS ONE",
   Year="2007",
   Volume="2",
   Pages="e384"
}


@article{klotz79,
	Author = {Lynn C. Klotz and Ned Komar and Roger L. Blanken and Ralph M. Mitchell},
	Journal = {PNAS},
	Pages = {4516-4520},
	Title = {Calculation of evolutionary trees from sequence data},
	Utilisateur = {Gilles Caraux},
	Volume = 76,
	Year = 1979}

@article{klotz81,
	Author = {Lynn C. Klotz and Roger L. Blanken},
	Journal = {Journal of Theoretical Biology},
	Pages = {261-272},
	Title = {A practical method for calculating evolutionary trees from sequence data},
	Utilisateur = {Gilles Caraux},
	Volume = 91,
	Year = 1981}

@article{kolaczkowski04,
	Author = {B. Kolaczkowski and J. Thornton},
	Journal = {Nature},
	Pages = {980-984},
	Title = {Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous},
	Volume = 431,
	Year = 2004}

@article{kondo93,
	Author = {Rumi Kondo and Satoshi Horai and Yoko Satta and Naoyuki Takahata},
	Journal = {Journal of Molecular Evolution},
	Pages = {517-531},
	Title = {Evolution of Hominoid Mitochondrial {DNA} with special Reference to the \\ Silent Substitution Rate over the Genome },
	Utilisateur = {Guillaume Andrieu},
	Volume = 36,
	Year = 1993}

@article{kondrashov02,
	Author = {A.S. Kondrashov and S. Sunyaev and F.A.  Kondrashov},
	Journal = {PNAS},
	Pages = {14878-14883},
	Title = {Dobzhansky-{M}uller incompatibilities in protein evolution},
	Volume = 99,
	Year = 2002}

@article{kosiol04,
	Author = {C. Kosiol and N. Goldman},
	Journal = {Molecular Biology and Evolution},
	Pages = {193-199},
	Title = {Different versions of the {D}ayhoff rate matrix},
	Volume = {22},
	Year = 2004}

@incollection{kruskal71,
	Author = {J. B. Kruskal and Isidor Dyen and Paul Black},
	Booktitle = {Mathematics in the archeological and     histor. sciences},
	Editor = {F. R. Hodson and D. G. Kendall and P. Tautu},
	Pages = {361-380},
	Publisher = {Edinburgh University Press},
	Title = {The vocabulary method of reconstructing language     trees: innovations and large-scale applications},
	Utilisateur = {Gilles Caraux},
	Year = 1971}

@article{kufels94,
	Author = {M. Kuhner and J. Felsenstein},
	Journal = {Molecular Biology and Evolution},
	Pages = {459-468},
	Title = {A simulation comparison of phylogeny algorithms     under equal and unequal evolutionary rates},
	Utilisateur = {Vincent},
	Volume = 11,
	Year = 1994}

@article{lanave84,
	Author = {C. Lanave and G. Preparata and C. Saccone and G. Serio},
	Journal = {Journal of Molecular Evolution},
	Pages = {86-93},
	Title = {A new method for calculating evolutionary substitution rates},
	Volume = 20,
	Year = 1984}

@article{lake87,
	Author = {James A. Lake},
	Journal = {Molecular Biology and Evolution},
	Pages = {167-191},
	Title = {A rate-independent technique for analysis of nucleic acid sequences : Evolutionary parsimony},
	Utilisateur = {Gilles Caraux},
	Volume = 4,
	Year = 1987}

@article{langley74,
	Author = {C. H. Langley and Walter M. Fitch},
	Journal = {Journal of Molecular Evolution},
	Pages = {161-177},
	Title = {An examination of the constancy of the rate of molecular evolution},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Volume = 3,
	Year = 1974}

@article{lanyon85,
	Author = {S. M. Lanyon},
	Journal = {Systematic Zoology},
	Number = 4,
	Pages = {397-403},
	Title = {Detecting internal inconsistencies in distance data},
	Utilisateur = {Vincent},
	Volume = 34,
	Year = 1985}

@article{larget99,
	Author = {B. Larget and D. L. Simon},
	Journal = {Molecular Biology and Evolution},
	Pages = {750-759},
	Title = {Markov Chain {M}onte {C}arlo algorithms for the bayesian analysis of phylogenetic trees},
	Volume = 16,
	Year = 1999}

@article{lartillot04,
	Author = {N. Lartillot and H. Philippe},
	Journal = {Molecular Biology and Evolution},
	Pages = {1095-1109},
	Title = {A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process},
	Volume = 21,
	Year = 2004}

@incollection{lausen86,
	Author = {Berthold Lausen and Paul O. Degens},
	Booktitle = {Die klassifikation und ihr umfeld},
	Editor = {Paul O. Degens and H. J. Hermes and O. Opitz},
	Pages = {306-314},
	Publisher = {Indeks Verlag},
	Series = {Studien zur Klassification},
	Title = {Variance estimation and the reconstruction of phylogenies},
	Utilisateur = {Gilles Caraux},
	Volume = 17,
	Year = 1986}

@incollection{lausen88,
	Author = {Berthold Lausen and Paul O. Degens},
	Booktitle = {Classification and related methods of data analysis},
	Editor = {H. H. Bock},
	Pages = {367-374},
	Publisher = {Elsevier},
	Title = {Evaluation of the reconstruction of phylogenies with {DNA-DNA}-Hybridization data},
	Utilisateur = {Gilles Caraux},
	Year = 1988}

@incollection{lausen89,
	Author = {Berthold Lausen},
	Booktitle = {Conceptual and numerical analysis of data},
	Editor = {O. Opitz},
	Pages = {481-488},
	Publisher = {Springer Verlag},
	Title = {Exploring homologous t{\sc rna} sequence data: positional mutation rates and genetic},
	Utilisateur = {Gilles Caraux},
	Year = 1989}

@article{lawrence97,
	Author = {J. Lawrence and H. Ochman},
	Journal = {Journal of Molecular Evolution},
	Pages = {383-397},
	Title = {Amelioration of bacterial genomes: rates of change and exchange},
	Volume = 44,
	Year = 1997}

@article{lawrence98,
	Author = {J. Lawrence and H. Ochman},
	Journal = {PNAS},
	Pages = {9413-9417},
	Title = {Molecular archaeology of the {\it \hbox{E}scherichia coli} genome},
	Volume = 95,
	Year = 1998}

@article{le08,
	Author = {SQ. Le and O. Gascuel},
	Journal = {Molecular Biology and Evolution},
	Title = {An Improved General Amino-Acid Replacement Matrix},
Volume = {25},
Pages = {1307-1320},
	Year = 2008}

@article{le_calve85,
	Author = {Georges {Le Calve}},
	Journal = {Statistiques et Analyse de Donn{\'e}es},
	Number = 2,
	Pages = {29-44},
	Title = {Distance {\`a} centre},
	Utilisateur = {Gilles Caraux},
	Volume = 10,
	Year = 1985}

@article{leclerc85a,
	Author = {Bruno Leclerc},
	Journal = {Math. Sci. hum.},
	Pages = {5-40},
	Title = {La comparaison des hierarchies : Indices et metriques},
	Utilisateur = {Gilles Caraux},
	Volume = 92,
	Year = 1985}

@article{leclerc85b,
	Author = {Bruno Leclerc},
	Journal = {Math. Sci. hum.},
	Pages = {5-34},
	Title = {La hi{\'e}rarchies de parties et leur demi-treillis},
	Utilisateur = {Gilles Caraux},
	Volume = 89,
	Year = 1985}

@article{leclerc94,
	Author = {Bruno Leclerc},
	Journal = {To appear in Journal of Classification},
	Title = {Minimum spanning trees for tree metrics :     abridgements and adjustements},
	Utilisateur = {Vincent},
	Year = 1994}

@article{lecointre93,
	Author = {G. Lecointre and H. Philippe      and H.L.V. L{\^e} and H. Le Guyader},
	Journal = {Mol. Phylogenet. Evol.},
	Pages = {205-224},
	Title = {Species sampling has a major impact on      phylogenetic inference},
	Volume = 2,
	Year = 1993}

@article{lemmon02,
	Author = {A. Lemmon and M. Milinkovitch},
	Journal = {PNAS},
	Pages = {10516-10521},
	Title = {The metapopulation genetic algorithm: an efficient solution for the problem of large phylogeny estimation},
	Volume = 99,
	Year = 2002}

@article{metapiga,
	Author = {A.R. Lemmon and Milinkovitch M.C.},
	Journal = {PNAS},
	Pages = {10516-10521},
	Title = {The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation},
	Volume = 99,
	Year = 2002}

@article{lee95,
	Author = {Y. Lee and T. Ota and V. Vaquier},
	Journal = {Molecular Biology and Evolution},
	Pages = {231-238},
	Title = {Positive selection is a general phenomenon in the evolution of abalone sperm lysin},
	Volume = 12,
	Year = 1995}

@Article{lepage06,
   Author="Lepage, T.  and Lawi, S.  and Tupper, P.  and Bryant, D. ",
   Title="{{C}ontinuous and tractable models for the variation of evolutionary rates}",
   Journal="Math Biosci",
   Year="2006",
   Volume="199",
   Pages="216--233",
   Month="Feb"
}


@article{lepage07,
	Author = {T. Lepage and D. Bryant and H. Philippe and N. Lartillot},
	Journal = {Molecular Biology and Evolution},
	Pages = {2669-2680},
	Title = {A general comparison of relaxed molecular clock models},
	Volume = 24,
	Year = 2007}

@article{lewis98,
	Author = {P. Lewis},
	Journal = {Molecular Biology and Evolution},
	Pages = {277-283},
	Title = {A genetic algorithm for maximum likelihood phylogeny inference using nucleotide sequence data},
	Volume = 15,
	Year = 1998}

@article{lewontin89,
	Author = {R. C. Lewontin},
	Journal = {Molecular Biology and Evolution},
	Pages = {15-32},
	Title = {Inferring the number of evolutionary events from                   {DNA} coding sequence differences},
	Utilisateur = {Gilles Caraux},
	Volume = 6,
	Year = 1989}

@inproceedings{li87,
	Author = {W.-H. Li and K.-H. Wolfe and J. Sourdis and P.M. Sharp},
	Booktitle = {Cold Spring Harbor Symposia on Quantitative Biology},
	Editor = {Cold Spring Harbore Laboratory},
	Pages = {847-856},
	Title = {Reconstruction of phylogenetic trees and estimation     of divergence times under nonconstant rates of evolution},
	Volume = {LII},
	Year = 1987}

@article{li89,
	Author = {Wen-Hsiung Li},
	Journal = {Molecular Biology and Evolution},
	Pages = {424-435},
	Title = {A statistical test of phylogenies estimated from sequence data},
	Utilisateur = {Gilles Caraux},
	Volume = 6,
	Year = 1989}

@incollection{li90,
	Address = {New York},
	Author = {Wen-Hsiung Li and Manolo Gouy},
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acid sequences},
	Chapter = 40,
	Editor = {Russsell F. Doolittle},
	Pages = {645-659},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Statistical Tests of Molecular Phylogenies},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@incollection{li91,
	Author = {Wen-Hsiung Li and Manolo Gouy},
	Booktitle = {Phylogenetic analysis of {DNA} sequences},
	Chapter = 12,
	Editor = {Michael M. Miyamoto and Joel Cracraft},
	Pages = {249-277},
	Publisher = {Oxford university press},
	Title = {Statistical methods for testing molecular phylogenies},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Year = 1991}

@article{li92,
	Author = {Wen-Hsiung Li and Bousquet, J},
	Journal = {Molecular Biology and Evolution},
	Pages = {1185-1189},
	Title = {Relative-Rate test for nucleotide substitutions between two lineages},
	Utilisateur = {G. Andrieu},
	Volume = 9,
	Year = 1992}

@article{li93,
	Author = {Wen-Hsiung Li},
	Journal = {Journal of Molecular Evolution},
	Pages = {96-99},
	Title = { Unbiased estimation of the rates of synonimous  and nonsynonimous substitution},
	Utilisateur = {Guillaume Andrieu},
	Volume = 36,
	Year = 1993}

@article{li94,
	Author = {W.-H. Li and A. Zharkikh},
	Journal = {Systematic Biology},
	Pages = {424-430},
	Title = {What is the bootstrap technique?},
	Utilisateur = {Vincent},
	Volume = 43,
	Year = 1994}

@article{li95,
	Author = {W.-H. Li and A. Zharkikh},
	Journal = {Systematic Biology},
	Pages = {49-63},
	Title = {Statistical tests of {DNA} phylogenies},
	Volume = 44,
	Year = 1995}

@phdthesis{li96,
	Author = {S. Li},
	School = {Ohio State University},
	Title = {Phylogenetic tree construction using {M}arkov chain {M}onte {C}arlo},
	Year = 1996}

@article{lin02,
	Author = {Y.-H. Lin and P. McLenachan and A. Gore and M. Phillips and R. Ota and M. Hendy and D. Penny},
	Journal = {Molecular Biology and Evolution},
	Pages = {2060-2070},
	Title = {Four new mitochondrial genomes, and the stability of evolutionary trees of mammals},
	Volume = 19,
	Year = 2002}

@article{lockhart94,
	Author = {P. Lockhart and M. Steel and M. Hendy and D Penny},
	Journal = {Molecular Biology and Evolution},
	Pages = {605-612},
	Title = {Recovering Evolutionary Trees under a More Realistic Model of Sequence},
	Volume = 11,
	Year = 1994}

@article{lockhart98,
	Author = {P. Lockhart and M. Steel and A. Barbrook and D. Huson and M. Charleston and C. Howe},
	Journal = {Molecular Biology and Evolution},
	Pages = {1183-1188},
	Title = {A covariotide model explains apparent  phylogenetic structure of oxygenic photosynthetic lineages},
	Volume = 15,
	Year = 1998}

@article{lockhart00,
	Author = {P. Lockhart and  D. Huson and U. Maier and M. Fraunholz and Y. Van de Peer and  A. Barbrook and C. Howe and M. Steel.},
	Journal = {Molecular Biology and Evolution},
	Pages = {835-838},
	Title = {How molecules evolve in eubacteria},
	Volume = 17,
	Year = 2000}

@article{lockhart05,
	Author = {P. Lockhart and M. Steel},
	Journal = {Systematic Biology},
	Pages = {948-951},
	Title = {A tale of two processes},
	Volume = 54,
	Year = 2005}

@article{lopez99,
	Author = {P. Lopez and P. Forterre and H. Philippe},
	Journal = {Journal of Molecular Evolution},
	Pages = {496-508},
	Title = {The root of the tree of life in the light of the covarion model},
	Volume = 49,
	Year = 1999}

@article{lopez02,
	Author = {P. Lopez and D. Casane and H. Philippe},
	Journal = {Molecular Biology and Evolution},
	Pages = {1-7},
	Title = {Heterotachy, an important process of protein evolution},
	Volume = 19,
	Year = 2002}

@article{lundy,
	Author = {M. Lundy},
	Journal = {Biometrika},
	Number = 1,
	Pages = {191-198},
	Title = {Applications of the annealing algorithm to combinatorial problems in statistics},
	Utilisateur = {Gilles Caraux and Fernando Carvalho},
	Volume = 72,
	Year = 1985}

@article{lundy,
	Author = {M. Lundy},
	Journal = {Biometrika},
	Number = 1,
	Pages = {191-198},
	Title = {Applications of the annealing algorithm to combinatorial problems in statistics},
	Utilisateur = {Gilles Caraux and Fernando Carvalho},
	Volume = 72,
	Year = 1985}

@article{lynch00,
	Author = {M. Lynch and J. Conery},
	Journal = {Science},
	Pages = {1151-1155},
	Title = {The evolutionary fate and consequences of duplicated genes},
	Volume = 290,
	Year = 2000}

@article{lynch03,
	Author = {M. Lynch and J. Conery},
	Journal = {Journal of Structural and Functional Genomics},
	Pages = {35-44},
	Title = {The evolutionary demography of duplicate genes},
	Volume = 3,
	Year = 2003}

@article{lynch03b,
	Author = {M. Lynch and J. Conery},
	Journal = {Science},
	Pages = {1401-1404},
	Title = {The origins of genome complexity},
	Volume = 302,
	Year = 2003}

@article{lynch04,
	Author = {M. Lynch and J. Conery},
	Journal = {Science},
	Pages = {978b},
	Title = {Reponse to Comment on \"The origins of genome complexity\"},
	Volume = 306,
	Year = 2004}

@article{maddison91,
	Author = {D. R. Maddison},
	Journal = {Syst Zool},
	Note = {interessant, grpes d'arbres relies entre eux},
	Number = 3,
	Pages = {315-328},
	Title = {The discovery and importance of multiple islands of     most parsimonious trees},
	Utilisateur = {Vincent},
	Volume = 40,
	Year = 1991}

@article{maddison97,
	Author = {D. Maddison and D. Swofford and W. Maddison},
	Journal = {Systematic Biology},
	Volume = 46,
	Number = 4,
	Pages = {590-621},
	Title = {{NEXUS}: an extensible file format for systematic information},
	Year = 1997}


@article{maidak94,
	Author = {B.L. Maidak and N. Larsen and M.J. McCaughey and R. Overbeek and G.J. Olsen and K. Fogel and J. Blandy and C.R. Woese},
	Journal = { Nucl. Acids. Res},
	Pages = {3485-3487},
	Title = {The {R}ibosomal {D}atabase {P}roject},
	Volume = 22,
	Year = 1994}

@article{maidak96,
	Author = {B.L. Maidak and G.J. Olsen and N. Larsen and R. Overbeek and M.J. McCaughey and C.R. Woese},
	Journal = { Nucl. Acids. Res},
	Pages = {82-85},
	Title = {The {R}ibosomal {D}atabase {P}roject ({RDP})},
	Volume = 24,
	Year = 1996}

@article{maidak97,
	Author = {B.L. Maidak and G.J. Olsen and N. Larsen and R. Overbeek and M.J. McCaughey and C.R. Woese},
	Journal = { Nucl. Acids. Res},
	Pages = {109-111},
	Title = {The {RDP} ({R}ibosomal {D}atabase {P}roject)},
	Volume = 25,
	Year = 1997}

@article{maidak99,
	Author = {B.L. Maidak and J.R. Cole and C.T. Parker and G.M. Garrity and N. Larsen and B. Li and T.G. Lilburn and M.J. McCaughey and  G.J. Olsen and R. Overbeek and S. Pramanik and T.M. Schmidt and J.M. Tiedje and CR Woese},
	Journal = { Nucl. Acids. Res},
	Pages = {171-173},
	Title = {A new version of the {RDP} ({R}ibosomal {D}atabase {P}roject)},
	Volume = 27,
	Year = 1999}

@article{maidak00,
	Author = {B. L. Maidak and J. R. Cole and T. G. Lilburn and C. T. Parker and P. R. Saxman and J. M. Stredwick and G. M. Garrity and B. Li and G. J. Olsen and S. Pramanik and T. M. Schmidt and J. M. Tiedje},
	Journal = {Nucl. Acids. Res},
	Pages = {173-174},
	Title = {The {RDP} ({R}ibosomal {D}atabase {P}roject) continues},
	Volume = 28,
	Year = 2000}

@article{maidak01,
	Author = {B. L. Maidak and J. R. Cole and T. G. Lilburn and C. T. Parker and P. R. Saxman and                    R. J. Farris and G. M. Garrity and G. J. Olsen and T. M. Schmidt and J. M. Tiedje},
	Journal = {Nucl. Acids. Res},
	Pages = {173-174},
	Title = {The {RDP}-II ({R}ibosomal {D}atabase {P}roject)},
	Volume = 29,
	Year = 2001}

@article{manske87,
	Author = { Charles L. Manske and David J. Chapman},
	Journal = {Journal of Molecular Evolution},
	Pages = {226-251},
	Title = {Nonuniformity of Nucleotide Substitution Rates in Molecular Evolution:  Computer Simulation and Analysis of 5S Ribosomal Sequences},
	Utilisateur = {Guillaume Andrieu},
	Volume = 26,
	Year = 1987}

@article{margush81,
	Author = {T. Margush and F.R. McMorris},
	Journal = {Bulletin of Math. Biol.},
	Number = 2,
	Pages = {239-244},
	Title = {Consensus n-trees},
	Volume = 43,
	Year = 1981}

@article{massingham05,
  title={Detecting amino acid sites under positive selection and purifying selection},
  author={Massingham, Tim and Goldman, Nick},
  journal={Genetics},
  volume={169},
  number={3},
  pages={1753--1762},
  year={2005},
  publisher={Genetics Soc America}
}

@phdthesis{mau96,
	Author = {B. Mau},
	School = {Wiscontin University},
	Title = {Bayesian phylogenetic inference via Markov Chain {M}onte {C}arlo methods},
	Year = 1996}

@article{meacham81,
	Author = {C. Meacham},
	Journal = {Taxon},
	Pages = {591-600},
	Title = {A manual method for character compatibility},
	Volume = 30,
	Year = 1981}

@article{metropolis53,
	Author = {N. Metropolis and A.W. Rosenbluth and M.N. Rosenbluth and A.H. Teller and E. Teller},
	Journal = {J. of Chem. Phys.},
	Pages = {1087-1092},
	Title = {Equation of State Calculations by Fast Computing Machines},
	Volume = 21,
	Year = 1953}

@article{messier97,
	Author = {W. Messier and C.-B. Stewart},
	Journal = {Nature},
	Pages = {151-154},
	Title = {Episodic adaptative evolution of primate lysozymes},
	Volume = 385,
	Year = 1997}

@article{misof02,
	Author = {B. Misof and C. Anderson and T. Buckley and D. Erpenbeck and A. Rickert and K. Misof},
	Journal = {Journal of Molecular Evolution},
	Pages = {330-340},
	Title = {An empirical analysis of mt 16S r{RNA} covarion-like evolution  in insects: site-specific rate variation is clustered and frequently  detected},
	Volume = 56,
	Year = 2002}

@article{mitchison95,
	Author = {G. Mitchison and R. Durbin},
	Journal = {Journal of Molecular Evolution},
	Pages = {1139-1151},
	Title = {Tree-based maximum likelihood substitution matrices and hidden Markov model},
	Volume = 41,
	Year = 1995}

@book{miyamoto91,
	Address = {New York - Oxford},
	Editor = {Michael M. Miyamoto and Joel Cracraft},
	Publisher = {Oxford University Press},
	Title = {{P}hylogenic {A}nalysis of {DNA} {S}equences},
	Utilisateur = {Guillaume Andrieu},
	Year = 1991}

@article{miyata81,
	Author = { Takashi Miyata and Teruo Yasunaga},
	Journal = {Genetics},
	Pages = {641-657},
	Title = {Molecular Evolution of m{RNA} : A Method for estimating  Evolutionary Rates of Synonymous and Amino Acid Substitutions from Homologous Nucleotide Sequences and its Application },
	Utilisateur = {Guillaume Andrieu},
	Volume = 98,
	Year = 1981}

@book{mood,
	Address = {Paris},
	Author = {Alexander Mood et Franklin A. Graybill},
	Publisher = {Dunod},
	Title = {Introduction a la {S}tatistique {T}heorique},
	Year = 1973}

@article{moore73,
	Author = {G. W. Moore, J. Barnabas, M. Goodman},
	Journal = {Journal of Theoretical Biology},
	Pages = {459-485},
	Title = {A Method For Constructing Maximum Parsimony     Ancestral Amino Acid Sequences on a Given Network},
	Volume = 38,
	Year = 1973}

@techreport{moulton96,
	Author = {V. Moulton and M.A. Steel},
	Institution = {Univ. of Canterbury},
	Number = 148,
	Title = {Retractions of finite distance functions onto tree metrics},
	Year = 1996}

@article{muller00,
	Author = {T. Muller and M. Vingron},
	Journal = {Journal of Computational Biology},
	Pages = {761-776},
	Title = {Modeling amino acid replacement.},
	Volume = 7,
	Year = 2000}

@article{mullis87,
	Author = {K.B. Mullis and F.A. Faloona},
	Journal = {Methods. in Enzym.},
	Pages = {335-350},
	Title = {Specific synthesis of {DNA} in vitro via polymerase                    catalyzed chained reaction},
	Volume = 155,
	Year = 1987}

@article{murphy01,
	Author = {W. J. Murphy and E. Eizirik and W. E. Johnson and Zhang Y.P. and O.A. Ryder and S.J. O'Brien},
	Journal = {Nature},
	Pages = {614-618},
	Title = {Molecular phylogenetics and the origins of placental mammals},
	Volume = 409,
	Year = 2001}

@article{murphy01b,
	Author = {M. Murphy and E. Eizirik and S. O'Brien and O. Madsen and M. Scally and C. Douady and E. Teeling and O. Ryder and M. Stanhope and W. de Jong and M. Springer},
	Journal = {Science},
	Pages = {2348-2351},
	Title = {Resolution of the early placental mammal radiation using Bayesian phylogenetics},
	Volume = 294,
	Year = 2001}

@article{muse94,
	Author = {S. Muse and B. Gaut},
	Journal = {Molecular Biology and Evolution},
	Pages = {715-724},
	Title = {A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome},
	Volume = 11,
	Year = 1994}

@incollection{muse95,
	Address = {Penn. State Univ.},
	Author = {S. V. Muse},
	Booktitle = {Current Topics on Molecular Evolution},
	Editor = {M. Nei and N. Takahata},
	Pages = {115-124},
	Publisher = {University Park},
	Title = {Evolutionary analyses when nucleotides do not evolve independently},
	Year = 1995}

@article{muse95b,
	Author = {S. Muse},
	Journal = {Genetics},
	Pages = {1429-1439},
	Title = {Evolutionary analyses of {DNA} sequences subject to constraints on secondary structure},
	Volume = 139,
	Year = 1995}

@article{otha93,
	Author = {T. Ohta},
	Journal = {Genetics},
	Pages = {1271-1276},
	Title = {Pattern of nucleotide substitutions in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication},
	Volume = 134,
	Year = 1993}

@article{navidi91,
	Author = {W. C. Navidi and G. A. Churchill and A. von Haeseler},
	Journal = {Molecular Biology and Evolution},
	Pages = {128-143},
	Title = {Methods for infering phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants},
	Utilisateur = {Gilles Caraux},
	Volume = 8,
	Year = 1991}

@article{navidi92,
	Author = {W. C. Navidi and L. Beckett-Lemus},
	Journal = {Molecular Biology and Evolution},
	Pages = {1163-1175},
	Title = {The effect of unequal transversion rates on the accuracy of evolutionary parsimony},
	Utilisateur = {Gilles Caraux},
	Volume = 9,
	Year = 1992}

@article{needleman70,
	Author = {S. G. Needleman and C. D. Wunsch},
	Journal = {Journal of Molecular Biology},
	Pages = {443-453},
	Title = {A general method applicable to the search for similarities in the amino acid sequence of two proteins},
	Volume = 48,
	Year = 1970}

@article{nei79,
	Author = {Masatoshi Nei and Wen Hsiung Li},
	Journal = {PNAS},
	Number = 10,
	Pages = {5269-5273},
	Title = {Mathematical model for studying genetic variation in terms of restriction endonucleases},
	Utilisateur = {Gilles Caraux},
	Volume = 76,
	Year = 1979}

@article{nei81,
	Author = {Masatoshi Nei and Fumo Tajima},
	Journal = {Genetics},
	Pages = {145-163},
	Title = {{DNA} polymorphism detectable by restriction endonucleases},
	Utilisateur = {Gilles Caraux},
	Volume = 97,
	Year = 1981}

@article{nei85,
	Author = {M. Nei and J. C. Stephens and N. Saitou},
	Journal = {Molecular Biology and Evolution},
	Pages = {66-85},
	Title = {Methods for computing the standard errors of branching points in an                    evolutionary tree and their application to molecular data from humans and apes},
	Volume = 2,
	Year = 1985}

@article{nei86,
	Author = {M. Nei and T. Gojobori},
	Journal = {Molecular Biology and Evolution},
	Pages = {418-426},
	Title = {Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions},
	Volume = 3,
	Year = 1986}

@article{nei89,
	Author = {Masatoshi Nei and L. Jin},
	Journal = {Molecular Biology and Evolution},
	Pages = {290-300},
	Title = {Variance of the averages numbers of substitutions within and between populations},
	Utilisateur = {Ne Obt},
	Volume = 6,
	Year = 1989}

@incollection{nei91,
	Author = {M. Nei},
	Booktitle = {Phylogenetic analysis of {DNA} sequences},
	Editor = {M.M. Miyamoto and J. Cracraft},
	Publisher = {Oxford Univ. Press},
	Title = {Relative efficiencies of different tree-making     methods for molecular data},
	Year = 1991}

@article{nei92,
	Author = {Masatoshi Nei},
	Journal = {Molecular Biology and Evolution},
	Number = 6,
	Pages = {1176-1178},
	Title = {Age of the common ancestor of Human Mitochondrial {DNA}},
	Utilisateur = {Gilles Caraux},
	Volume = 9,
	Year = 1992}

@article{newton04,
	Author = {M. Newton and A. Noueiry and D. Sarkar and P. Ahlquist},
	Journal = {Biostatistics},
	Pages = {155-176},
	Title = {Detecting differential expression with a semiparametric hierarchical mixture method},
	Volume = 5,
	Year = 2004}

@article{nielsen98,
	Author = {R. Nielsen and Z. Yang},
	Journal = {Genetics},
	Pages = {929-936},
	Title = {Likelihood models for detecting positively selected amino acid sites and application to the {HIV}-1 envelope gene},
	Volume = 148,
	Year = 1998}

@book{nutall04,
	Address = {Cambridge},
	Author = {G.H.F. Nutall},
	Publisher = {Cambridge Univ. Press},
	Title = {Blood immunity and blood relationship},
	Year = 1904}

@book{nr,
	Address = {Cambridge},
	Author = {W. Press and B. Flannery and S. Teukolsky and W. Vetterling},
	Publisher = {Press Syndicate of the University of Cambridge},
	Title = {Numerical Recipes in C.},
	Year = 1988}

@article{olsen94,
	Author = {G. Olsen and H. Matsuda and R. Hagstrom and R. Overbeek},
	Journal = {Computer Applications in the Biosciences (CABIOS)},
	Pages = {41-48},
	Title = {{fastDNAml}: a tool for construction of phylogenetic trees of {DNA} sequences using maximum likelihood},
	Volume = 10,
	Year = 1994}

@article{fastdnaml,
	Author = {G. J. Olsen and H. Matsuda and R. Hagstrom and R. Overbeek},
	Journal = {Computer Applications in the Biosciences (CABIOS)},
	Pages = {41-48},
	Title = {{fastDNAml}: a tool for construction of phylogenetic trees of {DNA} sequences using maximum likelihood},
	Volume = 10,
	Year = 1994}

@incollection{neyman71,
	Address = {New York},
	Author = {J. Neyman},
	Booktitle = {Statistical decision theory and related topics},
	Editor = {S. Gupta and J. Yackel},
	Pages = {1-27},
	Publisher = {Academic Press},
	Title = {Molecular studies of evolution: a source of novel statistical problems},
	Year = 1971}

@article{ota00,
	Author = {S. Ota and W.-H. Li},
	Journal = {Molecular Biology and Evolution},
	Pages = {1401-1409},
	Title = {{NJML}: a Hybrid Algorithm for the Neighbor-Joining and Maximum-Likelihood Methods},
	Volume = 17,
	Year = 2000}

@article{ota01,
	Author = {S. Ota and W.-H. Li},
	Journal = {Molecular Biology and Evolution},
	Pages = {1983-1992},
	Title = {{NJML+}: an extension of the {NJML} method to handle protein sequence data and computer software implementation},
	Volume = 18,
	Year = 2001}

@article{felsenstein1975,
  title={A pain in the torus: some difficulties with models of isolation by distance},
  author={Felsenstein, Joseph},
  journal={American Naturalist},
  pages={359--368},
  year={1975},
  publisher={JSTOR}
}


@article{ota00b,
	Author = {R. Ota and P. Waddell and M. Hasegawa and H. Shimodaira and H. Kishino},
	Journal = {Molecular Biology and Evolution},
	Pages = {798-803},
	Title = {Appropriate likelihood ratio tests and marginal distribution for evolutionary tree models with constraints on parameters},
	Volume = 17,
	Year = 2000}

@article{otto00,
	Author = {S. Otto and J. Whitton},
	Journal = {Annual Review of Genetics},
	Pages = {401-437},
	Title = {Polyploid incidence and evolution},
	Volume = 34,
	Year = 2000}

@book{page98,
	Address = {Osney Mead, Oxford},
	Author = {Roderick Page and Eward Holmes},
	Publisher = {Blackwell Science Ltd},
	Title = {Molecular Evolution: a phylogenetic approach},
	Year = 1998}

@article{pauplin00,
	Author = {Y. Pauplin},
	Journal = {Journal of Molecular Evolution},
	Pages = {41-47},
	Title = {Direct calculation of a tree length using a distance matrix},
	Volume = 51,
	Year = 2000}

@article{penny87,
	Author = {David Penny and Michael D. Hendy and I. M. Henderson},
	Journal = {Cold Spring Harbor Symposia on Quantitative Biology},
	Pages = {857-862},
	Title = {Reliability of Evolutionary Trees},
	Utilisateur = {Gilles Caraux},
	Volume = 52,
	Year = 1987}

@incollection{penny91,
	Author = {D. Penny and M.D. Hendy and M.A. Steel},
	Booktitle = {Phylogenetic analysis of {DNA} sequences},
	Editor = {M. M. Miyamoto and J. Cracraft},
	Pages = {155-183},
	Title = {Testing the theory of descent},
	Year = 1991}

@article{penny92,
	Author = {David Penny and Michael D. Hendy and Michael A. Steel},
	Journal = {Tree},
	Pages = {73-78},
	Title = {Progress with Methods for Constructing Evolutionary Trees},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu or Vincent},
	Volume = 7,
	Year = 1992}

@article{penny01,
	Author = {D. Penny and B. McComish and M. Charleston and M. Hendy},
	Journal = {Journal of Molecular Evolution},
	Pages = {711-723},
	Title = {Mathematical elegance with biochemical realism: the covarion model of molecular evolution},
	Volume = 53,
	Year = 2001}

@article{hobacgen,
	Author = {G. Perri{\`e}re and L. Duret and M. Gouy},
	Journal = {Genome Research},
	Pages = {379-385},
	Title = {{HOBACGEN}: database system for comparative genomics in bacteria},
	Volume = 10,
	Year = 2000}

@article{hovergen,
	Author = {L. Duret and D. Mouchiroud and M. Gouy},
	Journal = {Nucleic Acids Research},
	Pages = {2360-2365},
	Title = {{HOVERGEN}, a database of homologous vertebrate genes},
	Volume = 22,
	Year = 1994}

@article{li85,
	Author = {W.-H. Li and C.-I Wu and C.-C Luo},
	Journal = {Molecular Biology and Evolution},
	Pages = {150-174},
	Title = {A new method for estimating synonymous and non-synonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes},
	Volume = 2,
	Year = 1985}

@article{pagel04,
	Author = {M. Pagel and A. Meade},
	Journal = {Systematic Biology},
	Pages = {571-581},
	Title = {A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data},
	Volume = 53,
	Year = 2004}

@article{phillips02,
	Author = {M. Phillips and D. Penny},
	Journal = {Molecular Phylogenetics and Evolution},
	Pages = {171-185},
	Title = {The root of the mammalian tree inferred from whole mitochondrial genomes},
	Volume = 28,
	Year = 2002}

@article{philippe97,
	Author = {H. Philippe},
	Journal = {Journal of Molecular Evolution},
	Pages = {712-715},
	Title = {Rodent monophyly: pitfalls of molecular phylogenies},
	Volume = 45,
	Year = 1997}

@article{philippe00,
	Author = {H. Philippe and P. Lopez and H. Brinkman and K. Budin and A. Germot and J. Laurent and D. Moreira and M. Muller and H. Le Guyader},
	Journal = {Proceeding of the Royal Society B: Biological Sciences},
	Pages = {1213-1221},
	Title = {Early branching or fast evolving eukaryotes ? An answer based on slowly evolving positions},
	Volume = 267,
	Year = 2000}

@article{philippe00b,
	Author = {H. Philippe},
	Journal = {Protist},
	Pages = {307-316},
	Title = {Opinion : long branch attraction and protist phylogeny},
	Volume = 151,
	Year = 2000}

@article{philippe05,
	Author = {H. Philippe and Y. Zhou and H. Brinkmann and N. Rodrigue and F. Delsuc},
	Journal = {BMC Evolutionary Biology},
	Pages = {http://www.biomedcentral.com/1471-2148/5/50},
	Title = {Heterotachy and long-branch attraction in phylogenetics},
	Year = 2005}

@article{pollock99,
	Author = {D. Pollock and W. Taylor and N. Goldman},
	Journal = {Journal of Molecular Biology},
	Pages = {187-198},
	Title = {Co-evolving protein residues: maximum likelihood analysis and relationship to structure},
	Volume = 287,
	Year = 1999}

@article{posada98,
	Author = {D. Posada and K. Crandall},
	Journal = {Bioinformatics},
	Pages = {817-918},
	Title = {Modeltest: testing the model of {DNA} substitution},
	Volume = 14,
	Year = 1998}

@article{posada01,
  title={Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1)},
  author={Posada, D. and Crandall, K.A.},
  journal={Molecular Biology and Evolution},
  volume={18},
  number={6},
  pages={897--906},
  year={2001},
  publisher={SMBE}
}

@Article{poux06,
   Author="Poux, C.  and Chevret, P.  and Huchon, D.  and de Jong, W. W.  and Douzery, E. J. ",
   Title="{{A}rrival and diversification of caviomorph rodents and platyrrhine primates in {S}outh {A}merica}",
   Journal="Syst. Biol.",
   Year="2006",
   Volume="55",
   Pages="228--244",
   Month="Apr"
}


@techreport{prum92,
	Author = {Bernard Prum and Fran{{\c C}}ois Rodolphe and Elisabeth     de Turckheim},
	Institution = {INRA},
	Month = {October},
	Note = {{I}nfluence du {V}oisinage sur l'{E}volution d'une     {S{\'e}}quence d'{ADN}},
	Title = {{F}inding words with unexpected frequencies in     {DNA} sequences},
	Year = {1992}}

@article{pupko02,
	Author = {T. Pupko and N. Galtier},
	Journal = {Proceedings of The Royal Society B: Biological Sciences},
	Pages = {1313-1316},
	Title = {A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes},
	Volume = 269,
	Year = 2002}

@article{purvis97,
	Author = {A. Purvis and D. L. J. Quicke},
	Journal = {Trends in Ecology and Evolution},
	Number = 2,
	Pages = {49-50},
	Title = {Building phylogenies: are the big easy ?},
	Volume = 12,
	Year = 1997}

@article{qu83,
	Author = {L.H. Qu and B. Michot and J.P. Bachellerie},
	Journal = {Nucleic Acids Research},
	Pages = {5903-5920},
	Title = {Improved methods for structure probing in large                   RNAs: a rapid heterologous sequencing approach                   is coupled to the direct mapping of nuclease accessible                   sites. Application to the 5' terminal domain of eukaryotic},
	Volume = 11,
	Year = 1983}

@article{quesenberry64,
	Author = {C. P. Quesenberry and D. C. Hurst},
	Journal = {Technometrics},
	Month = {MAY},
	Number = 2,
	Pages = {191-195},
	Title = {Large Sample Simultaneous Confidence Intervals for     Multinomial Proportions },
	Volume = 6,
	Year = 1964}

@article{rannala96,
	Author = {B. Rannala and Z. Yang},
	Journal = {Journal of Molecular Evolution},
	Pages = {304-311},
	Title = {Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference},
	Volume = {43},
	Year = 1996}

@Article{rannala07,
   Author="Rannala, B.  and Yang, Z. ",
   Title="{{I}nferring speciation times under an episodic molecular clock}",
   Journal="Syst. Biol.",
   Year="2007",
   Volume="56",
   Pages="453--466",
   Month="Jun"
}

@article{ranwez01,
	Author = {V. Ranwez and O. Gascuel},
	Journal = {Molecular Biology and Evolution},
	Pages = {1103-11016},
	Title = {Quartet-based phylogenetic inference: improvements and limits.},
	Volume = {18},
	Year = 2001}

@article{ranwez02,
	Author = {V. Ranwez and O. Gascuel},
	Journal = {Molecular Biology and Evolution},
	Pages = {1952-1963},
	Title = {Improvement of Distance-Based Phylogenetic Methods by a Local Maximum Likelihood Approach Using Triplets},
	Volume = {19},
	Year = 2002}

@article{rasmol,
	Author = {R. Sayle and J. Milner-White},
	Journal = {Trends in Biochemical Sciences},
	Pages = {374},
	Title = {{R}as{M}ol: Biomolecular graphics for all},
	Volume = {20},
	Year = 1995}

@phdthesis{ranwezthese,
	Author = {V. Ranwez},
	School = {Universit{\'e} Montpellier II},
	Title = {M{\'e}thodes efficaces pour reconstruire des phylog{\'e}nies suivant le principe du maximum de vraisemblance},
	Year = 2002}

@article{rdp,
	Author = {B. L. Maidak and J.R. Cole and T.G. Lilburn and C.T. Parker Jr. and P.R. Saxman and R.J. Farris and G.M. Garrity and G.J. Olsen and T.M. Schmidt and J.M. Tiedje},
	Journal = {Nucleic Acids Research},
	Pages = {173-174},
	Title = {The {RDP}-II ({R}ibosomal {D}atabase {P}roject)},
	Volume = {29},
	Year = 2001}

@article{ren05,
	Author = {F. Ren and H. Tanaka and Z. Yang},
	Journal = {Systematic Biology},
	Pages = {808-818},
	Title = {An empirical examination of the utility of codon-substitution models in phylogeny reconstruction},
	Volume = 54,
	Year = 2005}

@book{renyi66,
	Address = {Paris},
	Author = {A. Renyi},
	Publisher = {Dunod},
	Title = {{C}alcul des {P}robabilites},
	Year = 1966}

@article{reyes98,
	Author = {A. Reyes and G. Pesole and C. Saccone},
	Journal = {Molecular Biology and Evolution},
	Pages = {499-505},
	Title = {Complete mitochondrial {DNA} sequence of the fat dormouse, {G}lis glis: further evidence of rodent paraphyly},
	Volume = {15},
	Year = {1998}}

@article{reyes00,
	Author = {A. Reyes and G. Pesole and C. Saccone},
	Journal = {Gene},
	Pages = {177-187},
	Title = {Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny},
	Volume = {259},
	Year = {2000}}

@article{reyes04,
	Author = {A. Reyes and C. Gissi and F. Catzeflis and E. Nevo and G. Pesole and C. Saccone},
	Journal = {Molecular Biology and Evolution},
	Pages = {397-403},
	Title = {Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods},
	Volume = {21},
	Year = {2004}}

@article{rice97,
	Author = {K. Rice and M. J. Donoghue and R. G. Olmstead},
	Journal = {Systematic Biology},
	Pages = {554-563},
	Title = {Analyzing large data sets: {\it rbcL} 500 revisited},
	Volume = {46},
	Year = {1997}}




@article{robinson71,
	Author = {D. Robinson},
	Journal = {J. Combinatorial Theory Ser B},
	Pages = {105-119},
	Title = {Comparison of labeled trees with valency three},
	Utilisateur = {Gilles Caraux},
	Volume = 11,
	Year = 1971}

@incollection{robinson79,
	Address = {Berlin},
	Author = {D. Robinson and L. Foulds},
	Booktitle = {Lectures Notes in Mathematics},
	Pages = {119-126},
	Publisher = {Springer},
	Title = {Comparison of weighted labeled trees},
	Utilisateur = {Gilles Caraux},
	Volume = 748,
	Year = 1979}

@article{robinson81,
	Author = {D. F. Robinson and L. R. Foulds},
	Journal = {Mathematical Biosciences},
	Pages = {131-147},
	Title = {Comparison of phylogenetic trees},
	Utilisateur = {Gilles Caraux et Vincent},
	Volume = 53,
	Year = 1981}

@Article{robinson98,
   Author="Robinson, M.  and Gouy, M.  and Gautier, C.  and Mouchiroud, D. ",
   Title="{{S}ensitivity of the relative-rate test to taxonomic sampling}",
   Journal="Molecular Biology and Evolution",
   Year="1998",
   Volume="15",
   Pages="1091--1098",
   Month="Sep"
}

@article{gharib13,
  title={The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in {GC}},
  author={Gharib, Walid H and Robinson-Rechavi, Marc},
  journal={Molecular Biology and Evolution},
  volume={30},
  number={7},
  pages={1675--1686},
  year={2013},
  publisher={SMBE}
}


@article{zhang05,
  title={Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level},
  author={Zhang, J. and Nielsen, R. and Yang, Z.},
  journal={Molecular Biology and Evolution},
  volume={22},
  number={12},
  pages={2472--2479},
  year={2005},
  publisher={SMBE}
}


@incollection{rodrigo01,
	Address = {Boston, Mass.},
	Author = {A. Rodrigo and E. Hanley and P. Goracke and G. Learn},
	Booktitle = {Computational and evolutionary analysis of HIV molecular sequences},
	Editor = {A. Rodrigo and G. Learn},
	Pages = {1-17},
	Publisher = {Kluwer Academic Publishers},
	Title = {Sampling and processing {HIV} molecular sequences : a computatinal evolutionary biologist's perspective},
	Year = 2001}

@article{rodriguez90,
	Author = {F. Rodriguez and J. L. Olivier and A. Marin and J. R. Medina},
	Journal = {Journal of Theoretical Biology},
	Pages = {485-501},
	Title = {The general stochastic model of nucleotide substitution},
	Volume = 142,
	Year = 1990}

@article{rodriguez03,
	Author = {F. Rodriguez-Trelles and R. Tarrio and F. Ayala},
	Journal = {PNAS},
	Pages = {13413-13417},
	Title = {Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene},
	Volume = {100},
	Year = {2003}}

@article{rogers99,
	Author = {J. Rogers and D. Swofford},
	Journal = {Molecular Biology and Evolution},
	Pages = {1079-1085},
	Title = {Multiple local maxima for likelihoods of phylogenetic trees: a simulation study},
	Volume = {16},
	Year = {1999}}

@article{rohlf74,
	Author = {F. James Rohlf},
	Journal = {Annual Review of Ecology and Systematics},
	Pages = {101-113},
	Title = {Methods of comparing classifications},
	Utilisateur = {Gilles Caraux},
	Volume = 5,
	Year = 1974}

@article{rosenberg01,
	Author = {M. Rosenberg and S. Kumar},
	Journal = {Molecular Biology and Evolution},
	Pages = {1823-1827},
	Title = {Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationship equally well},
	Volume = 19,
	Year = 2001}

@article{ross02,
	Author = {H. Ross and A. Rodrigo},
	Journal = {Journal of Virology},
	Pages = {11715-11720},
	Title = {Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration},
	Volume = 76,
	Year = 2002}

@book{ruegg,
	Address = {Lausanne},
	Author = {Alan Ruegg},
	Publisher = {Presses polytechniques romandes},
	Series = {Methodes mathematiques pour l'ingenieur},
	Title = {Processus Stochastiques},
	Year = 1989}


@Article{rutschmann07,
   Author="Rutschmann, F.  and Eriksson, T.  and Salim, K. A.  and Conti, E. ",
   Title="{{A}ssessing calibration uncertainty in molecular dating: the assignment of fossils to alternative calibration points}",
   Journal="Syst. Biol.",
   Year="2007",
   Volume="56",
   Pages="591--608",
   Month="Aug"
}

@incollection{gascuel07,
  Title={Modelling the variability of evolutionary processes},
  Author={Gascuel, O. and Guindon, S.},
  Editor={Olivier Gascuel and Mike Steel},
  Booktitle={Reconstructing Evolution: new mathematical and computational advances},
  Pages={65--99},
  Publisher={Oxford University Press},
  Year={2007}
}

@article{slatkin91,
  title={Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.},
  author={M. Slatkin and R. R. Hudson},
  journal={Genetics},
  volume={129},
  number={2},
  pages={555--562},
  year={1991},
  publisher={Genetics Soc America}
}


@article{rzhetsky92a,
	Author = {Andrey Rzhetsky and Masatoshi Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {945-967},
	Title = {A simple method for estimating and testing minimum-evolution trees},
	Utilisateur = {Olivier Gascuel et Guillaume Andrieu},
	Volume = 9,
	Year = 1992}

@article{rzhetsky92b,
	Author = {Andrey Rzhetsky and Masatoshi Nei },
	Journal = {Journal of Molecular Evolution},
	Pages = {367-375},
	Title = {Statistical Properties of the Ordinary Least-Squares, Generalized Least-Squares,  and Minimum-Evolution Methods of Phylogenetic Inference},
	Utilisateur = {Guillaume Andrieu},
	Volume = 35,
	Year = 1992}

@article{rzhetsky93,
	Author = {A. Rzhetsky and M. Nei },
	Journal = {Molecular Biology and Evolution},
	Pages = {1073-1095},
	Title = {Theoretical foundation of the minimum-evolution method of phylogenetic inference},
	Volume = 10,
	Year = 1993}

@article{rzhetsky94,
	Author = {A. Rzhetsky and M. Nei},
	Journal = {Journal of Molecular Evolution},
	Pages = {295-299},
	Title = {Unbiaised estimates of the number of nucleotide substitutions when substitution rate varies among different sites},
	Volume = 38,
	Year = 1994}

@article{rzhetsky95,
	Author = {A. Rzhetsky and S. Kumar and M. Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {163-167},
	Title = {Four-cluster analysis: a simple method to test phylogenetic                    hypotheses},
	Volume = 12,
	Year = 1995}

@article{rzhetsky95b,
	Author = {A. Rzhetsky},
	Journal = {Genetics.},
	Number = 2,
	Pages = {771-83},
	Title = {Estimating substitution rates in ribosomal RNA genes},
	Volume = 141,
	Year = 1995}

@article{rzhetsky96,
	Author = {A. Rzhetsky and T. Sitnikova},
	Journal = {Molecular Biology and Evolution},
	Pages = {1255-1265},
	Title = {When is it Safe to use an Oversimplified Substitution Model in Tree-Making?},
	Volume = 13,
	Year = 1996}

@incollection{saccone90,
	Address = {New York},
	Author = {Cecilia Saccone and Cecilia Lanave and Graziano Pesole and Giuliano Preperata  },
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acid sequences},
	Chapter = 35,
	Editor = {Russsell F. Doolittle},
	Pages = {570-583},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Influence of Base Composition on Quantitative Estimates of Gene Evolution},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@article{saccone91,
	Author = {Cecilia Saccone and Graziano Pesole and Elisabetta Sbis\'{a} },
	Journal = {Journal of Molecular Evolution},
	Pages = {88-91},
	Title = {the main regulatory region of mammalian mitochondria {DNA} : Stucture -function model and evilutionary pattern},
	Utilisateur = {G. Andrieu},
	Volume = 33,
	Year = 1991}

@article{saitou87,
	Author = {N. Saitou and M. Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {406-425},
	Title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees},
	Volume = 4,
	Year = 1987}

@article{nj,
	Author = {N. Saitou and M. Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {406-425},
	Title = {The neighbor-joining method: A new method for reconstruction phylogenetic trees},
	Utilisateur = {Gilles Caraux},
	Volume = 4,
	Year = 1987}

@article{saitou88,
	Author = {N. Saitou},
	Journal = {Journal of Molecular Evolution},
	Pages = {261-273},
	Title = {Property and efficiency of the maximum likelihood     method for molecular phylogeny},
	Utilisateur = {Gilles Caraux},
	Volume = 27,
	Year = 1988}

@article{saitou89,
	Author = {N. Saitou and T. Imanishi},
	Journal = {Molecular Biology and Evolution},
	Pages = {514-525},
	Title = {Relative efficiencies of the {F}itch-{M}argoliash,     {M}aximum-{P}arsimony, {M}aximum-{L}ikelihood,     {M}inimum-{E}volution, and {N}eighbor-{J}oining methods of     phylogenetic tree construction in obtaining the     correct tree},
	Volume = 6,
	Year = 1989}

@incollection{saitou90,
	Address = {New York},
	Author = {N. Saitou},
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acid sequences},
	Chapter = 36,
	Editor = {Russsell F. Doolittle},
	Pages = {584-598},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Maximum Likelihood Methods},
	Utilisateur = {Guillaume Andrieu},
	Volume = 183,
	Year = 1990}

@incollection{saitou91,
	Author = {N. Saitou},
	Booktitle = {Statistical Methods in Biological and Medical Sciences},
	Editor = {R. C. Rao and R. Chakraborty},
	Pages = {317-346},
	Publisher = {North-Holland},
	Series = {Handbook of Statistics},
	Title = {Statistical Methods for Phylogenetic Tree Reconstruction},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Volume = 8,
	Year = 1991}

@article{salter01,
	Author = {L. Salter and D. Pearl},
	Journal = {Systematic Biology},
	Pages = {7-17},
	Title = {Stochastic search strategy for estimation of maximum likelihood phylogenetic trees},
	Volume = 50,
	Year = 2001}

@article{sanderson94,
Author = {M. Sanderson and M. Donoghue and W. Piel and T. Eriksson},
Title = {Tree{BASE}: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life},
Journal = {American Journal of Botany},
Volume = 81,
Pages = {183},
Year = {1994}
}

@article{sanderson97,
	Author = {M. Sanderson},
	Journal = {Molecular Biology and Evolution},
	Pages = {1218-1231},
	Title = {A nonparametric approach to estimating divergence times in the absence of rate constancy},
	Volume = 14,
	Year = 1997}

@article{sanderson02,
	Author = {M. Sanderson},
	Journal = {Molecular Biology and Evolution},
	Pages = {101-109},
	Title = {Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach},
	Volume = 19,
	Year = 2002}

@article{sanger77,
	Author = {F. Sanger and S. Nicklen and A.R. Coulson},
	Journal = {PNAS},
	Pages = {5463-5467},
	Title = {DNA sequencing with chain-terminating inhibitors},
	Volume = 74,
	Year = 1977}

@article{sankoff94,
	Author = {D. Sankoff and Y. Abel and J. Hein},
	Journal = {Journal of Classification},
	Pages = {209-232},
	Title = {A tree - a hill; generalization of nearest-neighbor     in phylogenetic optimization},
	Utilisateur = {Vincent},
	Volume = 11,
	Year = 1994}

@inbook{saporta,
	Author = {G. Saporta},
	Chapter = { No 5 Notions {\'e}l{\'e}mentaires sur les processus al{\'e}atoires},
	Pages = {103-113},
	Publisher = {Technip},
	Title = {Probabilit{\'e}s analyse des donn{\'e}es et statistique},
	Utilisateur = {Guillaume Andrieu},
	Year = 1990}

@article{sharp97,
	Author = {P. Sharp},
	Journal = {Nature},
	Pages = {111-112},
	Title = {In search of molecular Darwinism},
	Volume = 385,
	Year = 1997}

@article{sharp87,
	Author = {P. Sharp and W.-H. Li},
	Journal = {Journal of Molecular Evolution},
	Pages = {1281-1295},
	Title = {The codon adaptation index--a measure of directional synonymous codon usage bias, and its potential applications},
	Volume = 15,
	Year = 1987}

@article{scherer89,
	Author = {Siegfried Scherer},
	Journal = {Molecular Biology and Evolution},
	Pages = {436-441},
	Title = {The relative-rate test of the molecular clock hypothesis : a note of caution},
	Utilisateur = {Gilles Caraux},
	Volume = 6,
	Year = 1989}

@article{shankarappa99,
	Author = {R. Shankarappa and J. Margolick and S. Gange and A. Rodrigo and D. Upchurch  and H. Farzadegan and P. Gupta and C. Rinaldo and G. Learn and X. He and X.-L Huang and J. Mullins },
	Journal = {Journal of Virology},
	Pages = {10489-10502},
	Title = {Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection},
	Volume = 73,
	Year = 1999}

@article{schoniger93,
	Author = {Michael Sch{\"o}niger and Arndt von Haesler },
	Journal = {Molecular Biology and Evolution},
	Pages = {471-483},
	Title = {A simple method to improve the reliability of tree reconstruction},
	Utilisateur = {G. Andrieu},
	Volume = 10,
	Year = 1993}

@article{schoniger94,
	Author = {M. Sch{\"o}niger and A. von Haesler },
	Journal = {Molecular Phylogeny and Evolution},
	Pages = {240-247},
	Title = {A stochastic model for the evolution of autocorrelated {DNA} sequences},
	Volume = 3,
	Year = 1994}

@article{schoniger95,
	Author = {M. Sch{\"o}niger and A. von Haesler },
	Journal = {Systematic Biology},
	Pages = {533-547},
	Title = {Performance of the maximum likelihood, neighbor joining, and maximum parsimony methods when sequence sites are not independent},
	Volume = 44,
	Year = 1995}

@article{schwarz78,
	Author = {G. Schwarz},
	Journal = {The annals of statistics},
	Pages = {461-464},
	Title = {Estimating the dimension of a model},
	Volume = 6,
	Year = 1978}

@article{sibley84,
	Author = {Charles G. Sibley and Jon E. Ahlquist},
	Journal = {Journal of Molecular Evolution},
	Pages = {2-15},
	Title = {the phylogeny of the hominoid primates, as indicated by {DNA-DNA} hybridization},
	Utilisateur = {Gilles Caraux},
	Volume = 20,
	Year = 1984}

@article{sibley87,
	Author = {Charles G. Sibley and Jon E. Ahlquist},
	Journal = {Journal of Molecular Evolution},
	Pages = {99-121},
	Title = {{DNA} hybridization evidence of hominoid phylogeny : results from expanded set},
	Utilisateur = {Gilles Caraux},
	Volume = 26,
	Year = 1987}

@book{paup,
	Address = {Sunderland, MA},
	Author = {D. Swofford},
	Publisher = {Sinauer},
	Title = {{PAUP$^*$}: Phylogenetic Analysis by Parsimony$^*$ and other methods},
	Year = 1999}

@book{bambe,
	Address = {Duquesne University},
	Author = {D. Simon and B. Larget},
	Publisher = {Department of Mathematics and Computer Science},
	Title = {Bayesian analysis in molecular biology and evolution (BAMBE), version 2.03 beta},
	Year = 2000}

@article{sarich67,
	Author = {V. Sarich and A. Wilson},
	Journal = {Science},
	Pages = {1200-1203},
	Title = {Immunological time scale for hominid evolution},
	Volume = 158,
	Year = 1967}

@article{self87,
	Author = {S. Self and K. Liang},
	Journal = {Journal of the American Statistical Association},
	Pages = {605--610},
	Title = {Asymptotic properties of maximum likelihood  estimators and likelihood ratio tests under  nonstandard conditions},
	Volume = 82,
	Year = 1987}

@article{shan09,
  title={Evolution of plant {MADS} box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications},
  author={Shan, H. and Zahn, L. and Guindon, S. and Wall, P.K. and Kong, H. and Ma, H. and DePamphilis, C.W. and Leebens-Mack, J. and others},
  journal={Molecular Biology and Evolution},
  volume={26},
  number={10},
  pages={2229--2244},
  year={2009},
  publisher={SMBE}
}
@article{murrell12,
  title={Detecting individual sites subject to episodic diversifying selection},
  author={Murrell, Ben and Wertheim, Joel O and Moola, Sasha and Weighill, Thomas and Scheffler, Konrad and Pond, Sergei L Kosakovsky},
  journal={PLoS Genetics},
  volume={8},
  number={7},
  pages={e1002764},
  year={2012},
  publisher={Public Library of Science}
}




@article{pond05,
  title={Not so different after all: a comparison of methods for detecting amino acid sites under selection},
  author={Kosakovsky Pond, Sergei   and Frost, Simon},
  journal={Molecular Biology and Evolution},
  volume={22},
  number={5},
  pages={1208--1222},
  year={2005},
  publisher={SMBE}
}


@article{shimodaira99,
	Author = {H. Shimodaira and M. Hasegawa},
	Journal = {Molecular Biology and Evolution},
	Pages = {1114-1116},
	Title = {Multiple comparisons of log-likelihoods with applications to phylogenetic inference},
	Volume = 16,
	Year = 1999}

@article{shriner04,
	Author = {D. Shrinner and A. Rodrigo and D. Nickle and J. Mullins},
	Journal = {Genetics},
	Pages = {1573-1583},
	Title = {Pervasive genomic recombination of {HIV-1} \mbox{\it in vivo}},
	Volume = {167},
	Year = 2004}

@article{sokal58,
	Author = {R. R. Sokal and C. D. Michener},
	Journal = {University of Kansas Science Bulletin},
	Pages = {1409-1438},
	Title = {A statistical method for evaluating systematic relationships},
	Volume = {38},
	Year = {1958}}

@article{sourdis87,
	Author = {J. Sourdis and C. Krimbas},
	Journal = {Molecular Biology and Evolution},
	Pages = {159-166},
	Title = {Accuracy of phylogenetic trees estimated from {DNA} sequence data},
	Volume = {4},
	Year = {1987}}

@article{springer01,
	Author = {M. Springer and R. De Bry and C. Douady and H. Amrine and O. Madsen and W. de Jong and M. Stanhope.},
	Journal = {Molecular Biology and Evolution},
	Pages = {132-143},
	Title = {Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction},
	Volume = {18},
	Year = {2001}}

@article{sourdis88,
	Author = {J. Sourdis and M. Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {298-311},
	Title = {Relative efficiencies of the maximum parsimony and distance-based methods in obtaining the correct phylogenetic tree},
	Volume = {5},
	Year = {1988}}

@article{srs,
	Author = {T. Etzold and P. Argos},
	Journal = {CABIOS},
	Pages = {49-57},
	Title = {{SRS}-an indexing and retrieval tool for flat file data libraries},
	Volume = {9},
	Year = {1993}}

@article{spencer05,
	Author = {M. Spencer and E. Susko and A. Roger},
	Journal = {Molecular Biology and Evolution},
	Pages = {1161-1164},
	Title = {Likelihood, parsimony, and heterogeneous evolution},
	Volume = {22},
	Year = {2005}}

@article{squires07,
author = {B. Squires and C. Macken and A. Garcia-Sastre and S. Godbole and J. Noronha and V. Hunt and R. Chang and C. Larsen and E. Klem and K. Biersack and R. Scheuermann},
title = {{B}io{H}ealth{B}ase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence},
journal = {Nucleic Acids Research},
volume = {Database issue},
year = {2007}
}



@article{raxml,
	Author = {A. Stamatakis},
	Journal = {Bioinformatics},
	Pages = {2688-2690},
	Title = {{RAxML-VI-HPC}: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models},
	Volume = 22,
	Year = 2006}

@article{stamatakis06,
	Author = {A. Stamatakis},
	Journal = {Bioinformatics},
	Pages = {2688-2690},
	Title = {{RAxML-VI-HPC}: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models},
	Volume = 22,
	Year = 2006}

@article{st77,
	Author = {S. Sattah and A. Tversky},
	Journal = {Psychometrika},
	Pages = {319-345},
	Title = {Additive similarity trees},
	Volume = 42,
	Year = 1977}

@article{steel92,
	Author = {M. Steel},
	Journal = {J. of Classification},
	Pages = {91-116},
	Title = {The complexity of reconstructing trees from     qualitative characters and subtrees},
	Utilisateur = {Vincent},
	Volume = 9,
	Year = 1992}

@article{steel93,
	Author = {M.A. Steel and D. Penny},
	Journal = {Systematic Biology},
	Number = 2,
	Pages = {126-141},
	Title = {Distributions of tree comparison metrics - some new results},
	Volume = 42,
	Year = 1993}

@article{steel94,
	Author = {M. Steel},
	Journal = {Systematic Biology},
	Pages = {560-564},
	Title = {The maximum likelihood point for a phylogenetic tree is not unique},
	Volume = 43,
	Year = 1994}

@article{steel00a,
	Author = {M. Steel and D. Penny},
	Journal = {Molecular Biology and Evolution},
	Pages = {839-50},
	Title = {Parsimony, likelihood, and the role of models in molecular phylogenetics},
	Volume = 17,
	Year = 2000}

@article{steel00b,
	Author = {M. Steel and D. Huson and P. Lockhart},
	Journal = {Systematic Biology},
	Pages = {225-232},
	Title = {Invariable site models and their use in phylogeny reconstruction},
	Volume = 49,
	Year = 2000}

@article{steel05,
	Author = {M. Steel},
	Journal = {Trends in Genetics},
	Pages = {307-309},
	Title = {Should phylogenetic models be trying to ``fit an elephant''?},
	Volume = 21,
	Year = 2005}

@incollection{stewart93,
	Author = {Caro-Beth Stewart},
	Booktitle = {Nature},
	Month = {february},
	Pages = {603-607},
	Title = {The Powers and pitfalls of parsimony},
	Utilisateur = {Vincent},
	Volume = 361,
	Year = 1993}

@article{stoffberg10,
author = {S. Stoffberg and D. Jacobs and I. Mackie and C. Matthee},
title = {Molecular phylogenetics and historical biogeography of Rhinolophus bats},
journal = {Molecular Phylogenetics and Evolution},
Volume = 54,
Pages = {1-9},
Year = 2010}


@article{strimmer96,
	Author = {K. Strimmer and A. von Haeseler},
	Journal = {Molecular Biology and Evolution},
	Pages = {964-969},
	Title = {Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies},
	Volume = 13,
	Year = 1996}

@article{strimmer97,
	Author = {K. Strimmer and N. Goldman and A. von Haeseler},
	Journal = {Molecular Biology and Evolution},
	Pages = {210-211},
	Title = {Baysian Probabilities and Quartet puzzling},
	Volume = 14,
	Year = 1997}

@article{strimmer00,
	Author = {K. Strimmer and V. Moulton},
	Journal = {Molecular Biology and Evolution},
	Pages = {875-881},
	Title = {Likelihood analysis of phylogenetic networks using directed graphical models},
	Volume = 17,
	Year = 2000}

@article{studier88,
	Author = {J. Studier and K. Kepler},
	Journal = {Molecular Biology and Evolution},
	Pages = {729-731},
	Title = {A note on the neighbor-joining algorithm of Saitou and Nei},
	Volume = 5,
	Year = 1988}

@article{sullivan95,
	Author = {J. Sullivan and K. E. Holsinger and C. Simon},
	Journal = {Molecular Biology and Evolution},
	Pages = {988-1001},
	Title = {Among-site variation and phylogenetic analysis of 12{S} r{RNA} in sigmontine rodents},
	Volume = 12,
	Year = 1995}

@article{sullivan97,
	Author = {J. Sullivan and D. Swofford},
	Journal = {Journal of Mammalian Evolution},
	Pages = {77-86},
	Title = {Are Guinea pigs Rodents? The importance of adequate models in molecular phylogenetics.},
	Volume = 4,
	Year = 1997}

@article{susko02,
	Author = {E. Susko and Y. Inagaki and C. Field and M. Holder and A. Roger},
	Journal = {Molecular Biology and Evolution},
	Pages = {1514-1523},
	Title = {Testing for differences in rates-across-sites distributions in phylogenetic subtrees},
	Volume = 19,
	Year = 2002}

@article{susko03,
	Author = {E. Susko and C. Field and C. Blouin and A. Roger},
	Journal = {Systematic Biology},
	Pages = {594-603},
	Title = {Estimation of rates-across-sites distributions in phylogenetic substitution models},
	Volume = 52,
	Year = 2003}

@article{suzuki99,
	Author = {Y. Suzuki and T. Gojobori},
	Journal = {Molecular Biology and Evolution},
	Pages = {1315-1328},
	Title = {A method for detecting positive selection at single amino acid sites},
	Volume = 16,
	Year = 1999}

@article{suzuki02,
	Author = {Y. Suzuki and G. V. Glazko and M. Nei},
	Journal = {PNAS},
	Pages = {16138-16143},
	Title = {Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics},
	Volume = 99,
	Year = 2002}

@article{suzuki04,
	Author = {Y. Suzuki and M. Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {914-921},
	Title = {False-positive selection identified by {ML}-based methods: examples from the {\it Sig1} gene of the diatom {T}halassoria weissflogii and the {\it tax} gene of a human {T}-cell lymphotropic virus},
	Volume = 21,
	Year = 2004}

@article{swanson01,
	Author = {W. Swanson and Z. Yang and M. Wolfner and C. Aquadro},
	Journal = {PNAS},
	Pages = {2509-2514},
	Title = {Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals},
	Volume = 98,
	Year = 2001}

@incollection{swofford90,
	Address = {Sunderland, MA},
	Author = {D. Swofford and G. Olsen},
	Booktitle = {Molecular Systematics},
	Chapter = 11,
	Editor = {D. M. Hillis and C. Moritz},
	Pages = {411-501},
	Publisher = {Sinauer},
	Title = {Phylogeny reconstruction},
	Year = 1990}

@incollection{swofford91,
	Author = {D. Swofford},
	Booktitle = {Phylogenetic analysis of {DNA} sequences},
	Chapter = 14,
	Editor = {M. M. Miyamoto and J. Cracraft},
	Pages = {295-333},
	Publisher = {Oxford University press},
	Title = {When are phylogeny estimates from molecular and     morphological data incongruent ?},
	Year = 1991}

@incollection{swofford96,
	Address = {Sunderland, MA},
	Author = {D. Swofford and G. Olsen and P. Waddel and D. Hillis},
	Booktitle = {Molecular Systematics},
	Chapter = 11,
	Editor = {D. Hillis and C. Moritz and B. Mable},
	Publisher = {Sinauer},
	Title = {Phylogenetic inference},
	Year = 1996}

@article{tajima82,
	Author = {Fumio Tajima and Masatoshi Nei },
	Journal = {Journal of Molecular Evolution},
	Pages = {115-120},
	Title = {Biases of the estimates of {DNA} divergence obtained by the restriction enzyme technique},
	Utilisateur = {Gilles Caraux},
	Volume = 18,
	Year = 1982}

@article{tajima84,
	Author = {Fumio Tajima and Masatoshi Nei },
	Journal = {Molecular Biology and Evolution},
	Pages = {269-285},
	Title = {Estimation of evolution distance between nucleotide     sequences},
	Volume = 1,
	Year = 1984}

@article{tajima92,
	Author = {Fumio Tajima },
	Journal = {Molecular Biology and Evolution},
	Pages = {168-181},
	Title = {Statistical Method for estimating the standard     errors of branch lengths in a phylognetic tree     reconstructed without assuming equal rates of     nucleotide substitution among different lineages},
	Utilisateur = {Guillaume Andrieu},
	Volume = 1,
	Year = 1992}

@article{tajima93,
	Author = {Fumio Tajima },
	Journal = {Molecular Biology and Evolution},
	Pages = {677-688},
	Title = {Unbiased Estimation of evolutionary distance between nucleotide sequences},
	Utilisateur = {Gilles Caraux and Guillaume Andrieu},
	Volume = 10,
	Year = 1993}

@article{tajima94,
	Author = {Fumio Tajima and Naoko Takezaki},
	Journal = {Molecular Biology and Evolution},
	Pages = {278-286},
	Title = {Estimation of Evolutionary Distance for Reconstructiong Molecular Phylogenetic Trees},
	Volume = 11,
	Year = 1994}

@article{takahashi00,
	Author = {Kei Takahashi and Masatoshi Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {1251-1258},
	Title = {Efficiencies of Fast Algorithms of Phylogenetic Inference Under the Criteria of Maximum Parsimony, Minimum Evolution, and Maximum Likelihood When a Large Number of Sequences Are Used},
	Volume = 17,
	Year = 2000}

@article{takahata81,
	Author = {Naoyuki Takahata and M. Kimura},
	Journal = {Genetics},
	Pages = {641-657},
	Title = {A Model of Evolutionary Base Substitutions and its Application with special Reference to rapid change of Pseudogenes},
	Utilisateur = {Guillaume Andrieu},
	Volume = 98,
	Year = 1981}

@article{takezaki94,
	Author = {N. Takezaki and M. Nei},
	Journal = {Journal of Molecular Evolution},
	Pages = {210-218},
	Title = {Inconsistency of the maximum parsimony method when     the rate of nucleotide, substitution is constant},
	Utilisateur = {Vincent},
	Volume = 39,
	Year = 1994}

@Article{takezaki95,
   Author="Takezaki, N.  and Rzhetsky, A.  and Nei, M. ",
   Title="{{P}hylogenetic test of the molecular clock and linearized trees}",
   Journal="Molecular Biology and Evolution",
   Year="1995",
   Volume="12",
   Pages="823--833",
   Month="Sep"
}

@article{tamura93,
	Author = {K. Tamura and M. Nei},
	Journal = {Molecular Biology and Evolution},
	Pages = {512-526},
	Title = {Estimation of the number of nucleotide substitutions in the control region of mitochondrial {DNA} in humans and chimpanzees},
	Volume = 10,
	Year = 1993}

@article{tateno82,
	Author = {Y. Tateno and M. Nei and F. Tajima},
	Journal = {Journal of Molecular Evolution},
	Pages = {387-404},
	Title = {Accuracy of Estimed Phylogenetic Trees from Molecular Data : I. Distantly Related Species},
	Volume = 18,
	Year = 1982}

@article{tavare86,
	Author = {S. Tavar\'e},
	Journal = {Lectures on Mathematics in the Life Sciences},
	Pages = {57-86},
	Title = {Some probabilistic and statistical problems on the analysis of {DNA} sequences},
	Volume = 17,
	Year = 1986}

@article{tillier98,
	Author = {E. Tillier and R. Collins},
	Journal = {Genetics},
	Pages = {1993-2002},
	Title = {High Apparent Rate of Simultaneous Compensatory Base-Pair Substitutions in Ribosomal RNA},
	Volume = 148,
	Year = 1998}

@article{clustal,
	Author = {J. Thompson and D. Higgins and T. Gibson },
	Journal = {Nucleic Acids Research},
	Pages = {4673-4680},
	Title = {{CLUSTAL W}: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice},
	Volume = 22,
	Year = 1994}

@article{clustalx,
	Author = {J. Thompson and T. Gibson and F. Plewniak and F. Jeanmougin and D. Higgins},
	Journal = {Nucleic Acids Research},
	Pages = {4876-4882},
	Title = {The {C}lustal{X} windows interface: flexible strategies for multiple sequences alignement aided by quality analysis tool},
	Volume = 24,
	Year = 1997}

@article{thorne91,
	Author = { J. L. Thorne and H. Kishino and J. Felsenstein},
	Journal = {Journal of Molecular Evolution},
	Pages = {114-124},
	Title = {An Evolutionary Model for Maximum Likelihood     Alignement of {DNA} Sequences},
	Volume = 33,
	Year = 1991}

@article{thorne92a,
	Author = { J. L. Thorne and H. Kishino and J. Felsenstein},
	Journal = {Journal of Molecular Evolution},
	Pages = {3-16},
	Title = {Inching toward Reality: an Improved Likelihood Model of Sequence Evolution},
	Volume = 34,
	Year = 1992}

@article{thorne92b,
	Author = {J. L. Thorne and H. Kishino },
	Journal = {Molecular Biology and Evolution},
	Pages = {1148-1162},
	Title = {Freeing Phylogenies from Artifacts of Alignement},
	Utilisateur = {G. Andrieu},
	Volume = 9,
	Year = 1992}

@article{thorne98,
	Author = {J. Thorne and H. Kishino and I. Painter},
	Journal = {Molecular Biology and Evolution},
	Pages = {1647-1657},
	Title = {Estimating the rate of evolution of the rate of molecular evolution},
	Volume = 15,
	Year = 1998}

@article{tourasse97,
	Author = {N.J. Tourasse and M. Gouy },
	Journal = {Molecular Biology and Evolution},
	Pages = {287-98},
	Title = {Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony},
	Volume = 14,
	Year = 1997}

@book{trivedi01,
	Address = {Chichester},
	Author = {K. Trivedi},
	Publisher = {Wiley},
	Title = {Probability and Statistics with Reliability, Queuing, and Computer Science Applications},
	Year = {2001}}

@article{tuffley98,
	Author = {C. Tuffley and M. Steel},
	Journal = {Mathematical Biosciences},
	Pages = {63-91},
	Title = {Modeling the covarion hypothesis of nucleotide substitution},
	Volume = 147,
	Year = 1998}

@incollection{vach89,
	Author = {Werner Vach},
	Booktitle = {Conceptual and numerical analysis of data},
	Editor = {O. Opitz},
	Pages = {230-238},
	Publisher = {Springer Verlag},
	Title = {Least squares approximation of additive trees},
	Year = 1989}

@article{wahlberg06,
Author = {N. Wahlberg},
Journal = {Systematic Biology},
Title = {That awkward age for butterflies: insights from the age of the butterfly subfamily {N}ymphalinae ({L}epidoptera: {N}ymphalidae)},
Pages = {703-714},
Volume = {55},
Year = {2006},
}

@article{wakeley93,
	Author = {J. Wakeley},
	Journal = {J Mol Evol},
	Number = 6,
	Pages = {613-23},
	Title = {Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA.},
	Volume = 37,
	Year = 1993}

@article{wakeley94,
	Author = {J. Wakeley},
	Journal = {Molecular Biology and Evolution},
	Pages = {436-442},
	Title = {Substitution rate variation among sites and the estimation of transition bias},
	Year = 1994}

@article{vandepeer04,
	Author = {Y. Van de Peer},
	Journal = {Nature Reviews Genetics},
	Pages = {752-763},
	Title = {Computational approaches to unveiling ancient genome duplications},
	Volume = 5,
	Year = 2004}

@article{vin04,
	Author = {L. Sy Vinh and A. von Haeseler},
	Journal = {Molecular Biology and Evolution},
	Pages = {1565-1571},
	Title = {{IQPNNI}: Moving Fast Through Tree Space and Stopping in Time},
	Volume = 21,
	Year = 2004}

@article{vonhaeseler93,
	Author = {Arndt Von Haeseler and Gary A. Churchill},
	Journal = {J. Mol Evol},
	Pages = {77-85},
	Title = {Network Models for Sequence Evolution},
	Utilisateur = {Guillaume Andrieu},
	Volume = 37,
	Year = 1993}

@article{wagner02,
	Author = {A. Wagner},
	Journal = {Genome Biology},
	Pages = {1012.1-1012.3},
	Title = {Selection and gene duplication : a view from the genome},
	Volume = 3,
	Year = 2002}

@phdthesis{waddell95,
	Author = {P.J. Waddell},
	School = {Massey University},
	Title = {Statisctical Methods of Phylogenetic Analysis: Including Hadamard Conjugations, LogDet Transforms, and Maximum Likelihood},
	Year = 1995}

@article{waterman77,
	Author = {M. S. Waterman and T. F. Smith and M. Singh and W. A. Beyer},
	Journal = {Journal of Theoretical Biology},
	Pages = {199-213},
	Title = {Additive Evolutonary trees},
	Utilisateur = {Gilles Caraux et Vincent},
	Volume = 64,
	Year = 1977}

@article{waterman78,
	Author = {M. S. Waterman and T. F. Smith},
	Journal = {Journal of Theoretical Biology},
	Pages = {789-800},
	Title = {On the similarity of dendrograms},
	Utilisateur = {Gilles Caraux},
	Volume = 73,
	Year = 1978}

@article{whelan01,
	Author = {S. Whelan and Pietro Li{\`o} and Nick Goldman},
	Journal = {Trends in Genetics},
	Number = 5,
	Pages = {262-272},
	Title = {Molecular phylogenetics: state-of-the art methods for looking into the past},
	Volume = 17,
	Year = 2001}

@article{whelan01b,
	Author = {S. Whelan and N. Goldman},
	Journal = {Molecular Biology and Evolution},
	Pages = {691-699},
	Title = {A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach},
	Volume = 18,
	Year = 2001}

@article{wilkinson95,
	Author = {M. Wilkinson},
	Journal = {Systematic Biology},
	Optnumber = {3},
	Optpages = {435-439},
	Optvolume = {44},
	Title = {More on reduced consensus methods},
	Year = {1995}}

@article{whitley94,
	Author = {D. Whitley},
	Journal = {Statistics and Computing},
	Pages = {65-85},
	Title = {A Genetic Algorithm Tutorial},
	Volume = 4,
	Year = {1994}}

@incollection{williams90,
	Address = {New York},
	Author = {Patrick L. Williams and Walter M. Fitch},
	Booktitle = {Molecular evolution : computer analysis of protein and nucleic acidsequences},
	Chapter = 38,
	Editor = {Russsell F. Doolittle},
	Pages = {615-626},
	Publisher = {Academic Press},
	Series = {Methods In Enzymology},
	Title = {Phylogeny Determination Using Dynamically Weighted Parsimony Method},
	Volume = 183,
	Year = 1990}

@article{suzuki08,
  title={False-positive results obtained from the branch-site test of positive selection},
  author={Suzuki, Yoshiyuki},
  journal={Genes \& Genetic Systems},
  volume={83},
  number={4},
  pages={331--338},
  year={2008},
  publisher={J-STAGE}
}

@article{nozawa09,
  title={Reliabilities of identifying positive selection by the branch-site and the site-prediction methods},
  author={Nozawa, Masafumi and Suzuki, Yoshiyuki and Nei, Masatoshi},
  journal={PNAS},
  volume={106},
  number={16},
  pages={6700--6705},
  year={2009},
  publisher={National Acad Sciences}
}

@article{wong04,
	Author = {W. Wong  and Z. Yang and N. Goldman and R. Nielsen},
	Journal = {Genetics},
	Pages = {1041-1051},
	Title = {Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites},
	Volume = {168},
	Year = 2004}

@article{yang11,
  title={Statistical properties of the branch-site test of positive selection},
  author={Yang, Ziheng and dos Reis, Mario},
  journal={Molecular Biology and Evolution},
  volume={28},
  number={3},
  pages={1217--1228},
  year={2011},
  publisher={SMBE}
}


@article{yang93,
	Author = {Z Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {1396-1401},
	Title = {Maximum-likelihood estimation of phylogeny from {DNA} sequences when substitution rates differ over sites},
	Volume = {10},
	Year = 1993}

@article{yang94,
	Author = {Z. Yang and N. Goldman and A. Friday},
	Journal = {Molecular Biology and Evolution},
	Pages = {316-324},
	Title = {Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.},
	Volume = 11,
	Year = 1994}

@article{yang94b,
	Author = {Z. Yang},
	Journal = {Journal of Molecular Evolution},
	Pages = {306-314},
	Title = {Maximum likelihood phylogenetic estimation from {DNA} sequences with variable rates over sites: approximate methods},
	Volume = 39,
	Year = 1994}

@article{yang94c,
	Author = {Z. Yang},
	Journal = {Journal of Molecular Evolution},
	Pages = {105-111},
	Title = {Estimating the pattern of nucleotide substitution},
	Volume = 10,
	Year = 1994}

@article{yang94d,
	Author = {Z. Yang},
	Journal = {Systematic Biology},
	Pages = {329-342},
	Title = {Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods},
	Volume = 43,
	Year = 1994}

@article{yang95a,
	Author = {Z. Yang},
	Journal = {Journal of Molecular Evolution},
	Pages = {689-697},
	Title = {Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites},
	Volume = 40,
	Year = 1995}

@article{yang95b,
	Author = {Z. Yang},
	Journal = {Genetics},
	Pages = {993-1005},
	Title = {A space-time process model for the evolution of {DNA} sequences},
	Volume = 193,
	Year = 1995}

@article{yang96,
	Author = {Z. Yang and S. Kumar},
	Journal = {Molecular Biology and Evolution},
	Pages = {650-659},
	Title = {Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites},
	Volume = 13,
	Year = 1996}

@article{yang98,
	Author = {Z. Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {568-573},
	Title = {Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution},
	Volume = 15,
	Year = 1998}

@article{paml,
	Author = {Z. Yang},
	Journal = {Computer Applications in the Biosciences (CABIOS)},
	Pages = {555-556},
	Title = {{PAML} : a program package for phylogenetic analysis by maximum likelihood},
	Volume = 13,
	Year = 1997}

@article{paml4,
  title={{PAML} 4: phylogenetic analysis by maximum likelihood},
  author={Yang, Ziheng},
  journal={Molecular Biology and Evolution},
  volume={24},
  number={8},
  pages={1586--1591},
  year={2007},
  publisher={SMBE}
}


@article{yang96b,
	Author = {Z. Yang},
	Journal = {Trends in Ecology and Evolution},
	Number = 9,
	Pages = {367-372},
	Title = {Among-site rate variation and its impact on phylogenetic analyses},
	Volume = 11,
	Year = 1996}

@article{yang96c,
	Author = {Z. Yang},
	Journal = {Journal of Molecular Evolution},
	Pages = {294-307},
	Title = {Phylogenetic analysis using parsimony and likelihood methods},
	Volume = 42,
	Year = 1996}

@article{yang97,
	Author = {Z. Yang},
	Journal = {Trends in Ecology and Evolution},
	Number = 9,
	Pages = {357},
	Title = {Are big trees indeed easy ?},
	Volume = 12,
	Year = 1997}

@article{yang97b,
	Author = {Z. Yang and B. Rannala},
	Journal = {Molecular Biology and Evolution},
	Pages = {717-724},
	Title = {Bayesian phylogenetic inference using {DNA} sequences: a Markov Chain {M}onte {C}arlo method},
	Volume = 14,
	Year = 1997}

@article{yang97c,
	Author = {Z. Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {105-108},
	Title = {How often do wrong models produce better phylogenies?},
	Volume = 14,
	Year = 1997}

@article{yang00,
	Author = {Z. Yang},
	Journal = {Journal of Molecular Evolution},
	Pages = {423-432},
	Title = {Maximum likelihood Estimation on large phylogenies and analysis of adaptative evolution in human influenza virus {A}},
	Volume = 51,
	Year = 2000}


@article{yang00d,
  title={Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites},
  author={Yang, Z. and Swanson, W.J. and Vacquier, V.D.},
  journal={Molecular Biology and Evolution},
  volume={17},
  number={10},
  pages={1446--1455},
  year={2000},
  publisher={SMBE}
}


@Article{yang06,
   Author="Yang, Z.  and Rannala, B. ",
   Title="{{B}ayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds}",
   Journal="Molecular Biology and Evolution",
   Year="2006",
   Volume="23",
   Pages="212--226",
   Month="Jan"
}




@book{yang06b,
  title={Computational molecular evolution},
  author={Yang, Z.},
  volume={284},
  year={2006},
  publisher={Oxford University Press Oxford}
}



@article{pond11,
  title={A random effects branch-site model for detecting episodic diversifying selection},
  author={Kosakovsky Pond, Sergei L  and Murrell, Ben and Fourment, Mathieu and Frost, Simon DW and Delport, Wayne and Scheffler, Konrad},
  journal={Molecular Biology and Evolution},
  volume={28},
  number={11},
  pages={3033--3043},
  year={2011},
  publisher={SMBE}
}



@article{yokoyama96,
	Author = {S. Yokoyama and R. Yokoyama},
	Journal = {Annual Review of Ecology and Systematics},
	Pages = {543-567},
	Title = {Adaptative evolution of photoreceptors and visual pigments in vertebrates},
	Volume = 27,
	Year = 1996}

@article{yang00b,
	Author = {Z. Yang and R. Nielsen},
	Journal = {Molecular Biology and Evolution},
	Pages = {32-43},
	Title = {Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models},
	Volume = 17,
	Year = 2000}

@article{yang00c,
	Author = {Z. Yang and R. Nielsen and N. Goldman and A.-M. {Krabbe Pedersen}},
	Journal = {Genetics},
	Pages = {431-449},
	Title = {Codon-substitution models for heterogeneous selection pressure at amino acid sites},
	Volume = 155,
	Year = 2000}

@article{yang02,
	Author = {Z. Yang and R. Nielsen},
	Journal = {Molecular Biology and Evolution},
	Pages = {908-917},
	Title = {Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages},
	Volume = 19,
	Year = 2002}

@article{yang05,
	Author = {Z. Yang and W. Wong and R. Nielsen},
	Journal = {Molecular Biology and Evolution},
	Pages = {1107-1118},
	Title = {Bayes empirical {B}ayes inference of amino acid sites under positive selection},
	Volume = 22,
	Year = 2005}

@article{tateno94,
	Author = {Y. Tateno and  N. Takezaki and M. Nei },
	Journal = {Molecular Biology and Evolution},
	Pages = {261-77},
	Title = {Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.},
	Volume = 11,
	Year = 1994}

@article{uzzell71,
	Author = {T. Uzzell and K. Corbin},
	Journal = {Science},
	Pages = {1089-1096},
	Title = {Fitting discrete probability distributions to evolutionary events},
	Volume = 172,
	Year = 1971}

@article{winter02,
	Author = {K.-U. Winter and H. Saedler and G. Theissen},
	Journal = {The Plant Journal},
	Pages = {457-475},
	Title = {On the origin of class {B} floral homeotic genes: functional substitution and dominant inhibition in {\em \uppercase{A}rabidopsis} by expression of an orthologue from the gymnosperm {\em \uppercase{G}netum}},
	Volume = 31,
	Year = 2002}

@article{zahn05,
	Author = {L. Zahn and J. Leebens-Mack and C. DePamphilis and H. Ma and G. Theissen},
	Journal = {Journal of Heredity},
	Pages = {225-240},
	Title = {To {B} or {N}ot to {B} a flower: the role of {DEFICIENS} and {GLOBOSA} orthologs in the evolution of the angiosperms},
	Volume = {96},
	Year = {2005}}

@article{zaretskii65,
	Author = {K. Zaretskii },
	Journal = {USpekHi Math. Nauk.},
	Pages = {90-92},
	Title = {Construction d'un arbre sur la base d'un ensemble de distances entre ses feuilles},
	Volume = 20,
	Year = 1965}

@article{zharkikh92a,
	Author = {Andrey Zharkikh and Wen-Hsiung Li },
	Journal = {Molecular Biology and Evolution},
	Pages = {1119-1147},
	Title = {Statistical properties of Bootstrap estimation of     phylogenies variability from nucleotide     sequences. {I.} Four Taxa with a molecular clock.},
	Volume = 9,
	Year = 1992}

@article{zharkikh92b,
	Author = { Andrey Zharkikh and Wen-Hsiung Li},
	Journal = {Journal of Molecular Evolution},
	Pages = {356-366},
	Title = {Statistical Properties of Bootstrap Estimation of     Phylogenetic Variability from Nucleotide Sequences:     {II.} Four Taxa without a Molecular Clock},
	Volume = 35,
	Year = 1992}

@article{zharkikh93,
	Author = {A. Zharkikh and W.-H. Li},
	Journal = {Systematic Biology},
	Pages = {113-125},
	Title = {Inconsistency of the Maximum Parsimony Method: The     Case of Five Taxa With a Molecular Clock},
	Utilisateur = {Vincent},
	Volume = 42,
	Year = 1993}

@article{zharkikh94,
	Author = {A. Zharkikh},
	Journal = {Journal of Molecular Evolution},
	Pages = {315-329},
	Title = {Estimation of evolutionary distance between nucleotide sequences},
	Volume = 39,
	Year = 1994}

@article{zharkikh95,
	Author = {A. Zharkikh and W.-H. Li},
	Journal = {Mol. Phylogenet. Evol.},
	Number = 1,
	Pages = {44-63},
	Title = {Estimation of confidence in phylogeny: the     complete-and-partial bootstrap technique},
	Utilisateur = {Vincent et Olivier},
	Volume = 4,
	Year = 1995}

@inbook{zuckerkandl62,
	Address = {Amsterdam},
	Author = {E. Zuckerkandl and L. Pauling},
        Editor = {M. Kasha and B. Pullman},
	Chapter = {Molecular disease, evolution, and genic heterogeneity},
	Pages = {189-225},
	Publisher = {Elsevier},
	Title = {Horizons in Biochemistry},
	Year = 1962}

@incollection{vach92,
	Author = {V. Vach},
	Booktitle = {Analysing and Modeling Data and Knowledge},
	Editor = {M. Shader},
	Pages = {141-150},
	Publisher = {Springer},
	Title = {The Jukes-Cantor Transformation and Additivity of Estimated Genetic Distances},
	Year = 1992}

@Article{wu85,
   Author="Wu, C. I.  and Li, W. H. ",
   Title="{{E}vidence for higher rates of nucleotide substitution in rodents than in man}",
   Journal="PNAS",
   Year="1985",
   Volume="82",
   Pages="1741--1745",
   Month="Mar"
}

@phdthesis{garli,
	Author = {D. Zwickl},
	School = {The University of Texas at Austin},
	Title = {Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion},
	Year = {2006}}
