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Bug#517165: marked as done (ITP: phyml -- Phylogenetic estimation using Maximum Likelihood)

Your message dated Fri, 01 May 2009 12:44:49 +0000
with message-id <E1Lzs6j-0002f0-Qk@ries.debian.org>
and subject line Bug#517165: fixed in phyml 30042009-1
has caused the Debian Bug report #517165,
regarding ITP: phyml -- Phylogenetic estimation using Maximum Likelihood
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
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517165: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=517165
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message ---
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+

--- 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:

  to pool/main/p/phyml/phyml_30042009-1.diff.gz
  to pool/main/p/phyml/phyml_30042009-1.dsc
  to pool/main/p/phyml/phyml_30042009-1_amd64.deb
  to pool/main/p/phyml/phyml_30042009.orig.tar.gz

A summary of the changes between this version and the previous one is

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
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)

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>
 phyml      - Phylogenetic estimation using Maximum Likelihood
Closes: 517165
 phyml (30042009-1) unstable; urgency=low
   * Initial release (Closes: #517165)
 7d11108a1e25e07e2681b558fefdd2191e16d49e 1284 phyml_30042009-1.dsc
 fe297e6b3aace980d53eee3f6c1d6d82a8a47d24 879312 phyml_30042009.orig.tar.gz
 a81e214dfdf6c0ab3fb49366c5b550d0c72b6374 3672 phyml_30042009-1.diff.gz
 c516e9f98a157fdb8d4622ff6bee2a5ff422cb95 614520 phyml_30042009-1_amd64.deb
 8ecfd58b9eb25a69a8963831d258f572ed44e7a472bb7070d52289e22f1822a9 1284 phyml_30042009-1.dsc
 a7b3451e62c5d04b7f204778b78b489587c646d2ab4b6c1ba66cc18238eef249 879312 phyml_30042009.orig.tar.gz
 92795ab2b0489b64725dfc700aa1a61cad27826086e25636f5a85bd16c19e8c8 3672 phyml_30042009-1.diff.gz
 26a48113e8c87390520e3273ff9deea64498896ba0a28bc945144aea26720e56 614520 phyml_30042009-1_amd64.deb
 c7e345f548ad9b9ca722f2d09a63dd58 1284 science optional phyml_30042009-1.dsc
 1f6ee9787e7cc5030974eb1ba3968493 879312 science optional phyml_30042009.orig.tar.gz
 b084b671a71fac68429e113ff67d2e28 3672 science optional phyml_30042009-1.diff.gz
 1584017b29759cbeb68bb6c487120d2e 614520 science optional phyml_30042009-1_amd64.deb

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--- End Message ---

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