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 Clustal Omega for multiple sequence alignment, and also allows to use any external alignment algorithm able to read and write FASTA-formatted files.
* Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites.
* 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 3.1.
* Seaview can use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees.
* Seaview uses the Treerecs method to reconcile gene and species trees.
* SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.
* SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.