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

1) SeaView reads and writes various file formats (NEXUS, MSF,
   CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences
   and of phylogenetic trees.

2) SeaView drives programs muscle or clustalw for multiple sequence
   alignment, and also allows to use any external alignment algorithm
   able to read and write FASTA-formatted files.

3) Seaview drives the Gblocks program to select blocks of
   evolutionarily conserved sites.

4) SeaView computes phylogenetic trees by
	a) parsimony, using PHYLIP's dnapars/protpars algorithm,
	b) distance, with NJ or BioNJ algorithms on a variety of
	   evolutionary distances,
	c) maximum likelihood, driving program PhyML 3.0.

5) SeaView draws phylogenetic trees on screen, PDF or PostScript files
6) SeaView allows to download sequences from EMBL/GenBank/UniProt
   using the Internet.

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.

This requires fltk13. You will also need clustalw, Gblocks, PhyML, and
muscle, all of which SeaView drives.