--- Begin Message ---
- To: Debian Bug Tracking System <submit@bugs.debian.org>
- Subject: ITP: phyml -- Phylogenetic estimation using Maximum Likelihood
- From: Charles Plessy <plessy@debian.org>
- Date: Thu, 26 Feb 2009 14:19:05 +0900
- Message-id: <20090226051905.23905.66508.reportbug@anx159.gsc.riken.jp>
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
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+
--- End Message ---
--- Begin Message ---
Source: phyml
Source-Version: 30042009-1
We believe that the bug you reported is fixed in the latest version of
phyml, which is due to be installed in the Debian FTP archive:
phyml_30042009-1.diff.gz
to pool/main/p/phyml/phyml_30042009-1.diff.gz
phyml_30042009-1.dsc
to pool/main/p/phyml/phyml_30042009-1.dsc
phyml_30042009-1_amd64.deb
to pool/main/p/phyml/phyml_30042009-1_amd64.deb
phyml_30042009.orig.tar.gz
to pool/main/p/phyml/phyml_30042009.orig.tar.gz
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 517165@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <plessy@debian.org> (supplier of updated phyml package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Fri, 01 May 2009 08:53:44 +0900
Source: phyml
Binary: phyml
Architecture: source amd64
Version: 30042009-1
Distribution: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Closes: 517165
Changes:
phyml (30042009-1) unstable; urgency=low
.
* Initial release (Closes: #517165)
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Files:
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