2020-04-24 23:36:52 +00:00
|
|
|
{ stdenv, fetchurl, coreutils, fltk, libjpeg }:
|
|
|
|
|
|
|
|
|
|
stdenv.mkDerivation rec {
|
2020-07-18 16:06:22 +00:00
|
|
|
version = "5.0.4";
|
2020-04-24 23:36:52 +00:00
|
|
|
pname = "seaview";
|
|
|
|
|
|
|
|
|
|
src = fetchurl {
|
|
|
|
|
url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz";
|
2020-07-18 16:06:22 +00:00
|
|
|
sha256 = "09yp8467h49qnj7gg0mbcdha4ai3bn6vgs00gb76dd6h3pzfflz1";
|
2020-04-24 23:36:52 +00:00
|
|
|
};
|
|
|
|
|
|
|
|
|
|
buildInputs = [ fltk libjpeg ];
|
|
|
|
|
|
|
|
|
|
patchPhase = "sed -i 's#PATH=/bin:/usr/bin rm#'${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;
|
|
|
|
|
};
|
|
|
|
|
}
|
