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SeaView is a multiplatform, graphical user interface for multiple
sequence alignment and molecular phylogeny. Features:
- 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
- Can use the Transfer Bootstrap Expectation method to compute the
bootstrap support of PhyML and distance trees.
- Uses the Treerecs method to reconcile gene and species trees.
- Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript
files.
- Allows to download sequences from EMBL / GenBank / UniProt.
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.
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