SeaView is a multiplatform, graphical user interface for multiple
sequence alignment and molecular phylogeny. Features:

- Reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA,
  PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic
  trees.
- Drives programs muscle or Clustal Omega for multiple sequence
  alignment, and also allows to use any external alignment
  algorithm able to read and write FASTA-formatted files.
- Drives the Gblocks program to select blocks of evolutionarily
  conserved sites.
- Computes phylogenetic trees by parsimony, using PHYLIP's dnapars /
  protpars algorithm, distance, with NJ or BioNJ algorithms on a variety
  of evolutionary distances, maximum likelihood, driving program PhyML
- Can use the Transfer Bootstrap Expectation method to compute the
  bootstrap support of PhyML and distance trees.
- Uses the Treerecs method to reconcile gene and species trees.
- Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript
  files.
- Allows to download sequences from EMBL / GenBank / UniProt.

For details and citation:
Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
multiplatform graphical user interface for sequence alignment and
phylogenetic tree building. Molecular Biology and Evolution
27(2):221-224.