SeaView is a multi-platform, graphical user interface for multiple sequence alignment and molecular phylogeny.
SeaView drives the Muscle, Clustal Omega, Gblocks, and PhyML programs and uses code from the PHYLIP package for parsimony.
SeaView uses the FLTK project for its user interface.
- 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.
- Use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees.
- Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.
- Download sequences from EMBL/GenBank/UniProt using the Internet.
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