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 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 prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files. - SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet. Seaview is published in: 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.