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The nixpkgs-unstable channel's programs.sqlite was used to identify packages producing exactly one binary, and these automatically added to their package definitions wherever possible.
43 lines
2.1 KiB
Nix
43 lines
2.1 KiB
Nix
{ lib, stdenv, fetchurl, coreutils, fltk, libjpeg }:
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stdenv.mkDerivation rec {
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version = "5.0.5";
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pname = "seaview";
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src = fetchurl {
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url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz";
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sha256 = "sha256-zo9emLpHiDv6kekbx55NOibxWN2Zg7XngzGkUqSx+PI=";
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};
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buildInputs = [ fltk libjpeg ];
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patchPhase = "sed -i 's#PATH=/bin:/usr/bin rm#'${coreutils}/bin/rm'#' seaview.cxx";
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installPhase = "mkdir -p $out/bin; cp seaview $out/bin";
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meta = with lib; {
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description = "GUI for molecular phylogeny";
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mainProgram = "seaview";
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longDescription = ''
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SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.
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- SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.
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- 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.
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- Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites.
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- SeaView computes phylogenetic trees by
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+ parsimony, using PHYLIP's dnapars/protpars algorithm,
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+ distance, with NJ or BioNJ algorithms on a variety of evolutionary distances,
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+ maximum likelihood, driving program PhyML 3.1.
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- Seaview can use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees.
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- SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.
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- SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.
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Seaview is published in:
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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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'';
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homepage = "https://doua.prabi.fr/software/seaview";
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license = licenses.gpl3;
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maintainers = [ maintainers.iimog ];
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platforms = platforms.linux;
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};
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}
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