Seaview

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

SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.
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.
SeaView 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 3.0.
SeaView draws phylogenetic trees on screen, PDF or PostScript files (and prints them with the Mac and MSWindows versions).
SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.