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diff --git a/academic/seaview/README b/academic/seaview/README index 70a537171c..2fd0c66479 100644 --- a/academic/seaview/README +++ b/academic/seaview/README @@ -1,28 +1,22 @@ SeaView is a multiplatform, graphical user interface for multiple -sequence alignment and molecular phylogeny. Important features are: +sequence alignment and molecular phylogeny. Features: -1) SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, - FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of - phylogenetic trees. - -2) SeaView drives programs muscle or Clustal Omega (clustalo) for - multiple sequence alignment, and also allows to use any external - alignment algorithm able to read and write FASTA-formatted files. - -3) Seaview drives the Gblocks program to select blocks of - evolutionarily conserved sites. - -4) SeaView computes phylogenetic trees by - a) parsimony, using PHYLIP's dnapars/protpars algorithm - b) distance, with NJ or BioNJ algorithms on a variety of - evolutionary distances, - c) maximum likelihood, driving program PhyML - -5) SeaView prints and draws phylogenetic trees on screen, SVG, PDF or - PostScript files. - -6) SeaView allows to download sequences from EMBL/GenBank/UniProt - using the Internet. +- 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. +- 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 |