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Old 02-26-2009, 04:19 AM
Charles Plessy
 
Default 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: ${shlibsepends}, ${miscepends}
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
Upstream-Maintainer:
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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