SeaView is a multi-platform GUI for multiple sequence alignment and molecular
phylogeny. You can align DNA/protein sequences from several organisms, and find
out their relative positions in phylogenic tree.

* 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 3.1
* 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 using the Internet.

Once SeaView is installed, you can open the on-line help window through the
'Help' button to learn how to use SeaView.

Example MASE files are here: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
