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Bug#517165: ITP: phyml -- Phylogenetic estimation using Maximum Likelihood

Package: wnpp
Severity: wishlist
Owner: Charles Plessy <plessy@debian.org>

Hello everybody,

I intend to package Phyml, as it is necessary for upgrading SeaView to version
4.0.  As usual, the source of the PDF manual was omitted from the Upstream
tarball. I am working on this issue.

Have a nice day,

-- Charles

Source: phyml
Section: science
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy@debian.org>
Build-Depends: debhelper (>= 7), automake, autoconf
Standards-Version: 3.8.0
Homepage: http://www.atgc-montpellier.fr/phyml

Package: phyml
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: Phylogenetic estimation using Maximum Likelihood
 PhyML is a software that estimates maximum likelihood phylogenies from
 alignments of nucleotide or amino acid sequences. It provides a wide range of
 options that were designed to facilitate standard phylogenetic analyses. The
 main strengths of PhyML lies in the large number of substitution models coupled
 to various options to search the space of phylogenetic tree topologies, going
 from very fast and efficient methods to slower but generally more accurate
 approaches. It also implements two methods to evaluate branch supports in a
 sound statistical framework (the non-parametric bootstrap and the approximate
 likelihood ratio test).
 PhyML was designed to process moderate to large data sets. In theory,
 alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In
 practice however, the amount of memory required to process a data set is
 proportional of the product of the number of sequences by their length. Hence,
 a large number of sequences can only be processed provided that they are short.
 Also, PhyML can handle long sequences provided that they are not numerous. With
 most standard personal computers, the “comfort zone” for PhyML generally lies
 around 3 to 500 sequences less than 2,000 character long.

Upstream-Name: PhyML
 Stephane Guindon <guindon@stat.auckland.ac.nz>
 Department of Statistics. University of Auckland. New Zealand
 Universite Montpellier II - CNRS UMR 5506. LIRMM. Montpellier France.
 Olivier Gascuel <gascuel@lirmm.fr>
 Universite Montpellier II - CNRS UMR 5506. LIRMM. Montpellier France.
 Jean-Francois Dufayard <jeanfrancois.dufayard@gmail.com>
 Universite Montpellier II - CNRS UMR 5506. LIRMM. Montpellier France.
Upstream-Source: http://phyml.googlecode.com/files/phyml_3December2008.tar.gz

Files: *
Copyright: Stephane Guindon <guindon@stat.auckland.ac.nz>
           Olivier Gascuel <gascuel@lirmm.fr>
           Jean-Francois Dufayard <jeanfrancois.dufayard@gmail.com>
           Wim Hodrijk <wim@santafe.edu>
           Franck Lethiec <lethiec@lirmm.fr>
Licence: GPL-2+

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