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diff --git a/academic/seaview/README b/academic/seaview/README index 21de5ab1c5..7b3a2aa174 100644 --- a/academic/seaview/README +++ b/academic/seaview/README @@ -1,32 +1,32 @@ -SeaView is a multiplatform, graphical user interface for multiple +SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. Important features are: -1) SeaView reads and writes various file formats (NEXUS, MSF, - CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences +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 clustalw for multiple sequence - alignment, and also allows to use any external alignment algorithm + +2) SeaView drives programs muscle or clustalw 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 + +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 + b) distance, with NJ or BioNJ algorithms on a variety of evolutionary distances, c) maximum likelihood, driving program PhyML 3.0. - + 5) SeaView draws phylogenetic trees on screen, PDF or PostScript files -6) SeaView allows to download sequences from EMBL/GenBank/UniProt +6) SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet. 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. +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. -This requires fltk as a build dependency, but you also need clustalw, -Gblocks, PhyML, and muscle, all of which SeaView drives. +This requires fltk13. You will also need clustalw, Gblocks, PhyML, and +muscle, all of which SeaView drives. |