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{ stdenv, fetchurl, coreutils, fltk, libjpeg }:
stdenv.mkDerivation rec {
version = "5.0.2";
pname = "seaview";
src = fetchurl {
url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz";
sha256 = "0bad0nd18a36g6ysx28j68rbnwqn33ra8inx2lv2igqqcs6i5kif";
};
buildInputs = [ fltk libjpeg ];
patchPhase = "sed -i 's#PATH=/bin:/usr/bin rm#'${coreutils}/bin/rm'#' seaview.cxx";
installPhase = "mkdir -p $out/bin; cp seaview $out/bin";
meta = with stdenv.lib; {
description = "GUI for molecular phylogeny";
longDescription = ''
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.
'';
homepage = "http://doua.prabi.fr/software/seaview";
license = licenses.gpl3;
maintainers = [ maintainers.iimog ];
platforms = platforms.linux;
};
}
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