Your message dated Tue, 18 Jul 2017 10:00:15 +0000
with message-id <e1dxpid-0000gn...@fasolo.debian.org>
and subject line Bug#864823: fixed in python-treetime 0.0+20170607-1
has caused the Debian Bug report #864823,
regarding ITP: python-treetime -- inference of time stamped phylogenies and
ancestral reconstruction
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.
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immediately.)
--
864823: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=864823
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <ti...@debian.org>
* Package name : python-treetime
Version : 0.0+20170607
Upstream Author : Pavel Sagulenko and Richard Neher
* URL : https://github.com/neherlab/treetime
* License : MIT
Programming Lang: Python
Description : inference of time stamped phylogenies and ancestral
reconstruction
TreeTime provides routines for ancestral sequence reconstruction and the
maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
where all branches are scaled such that the locations of terminal nodes
correspond to their sampling times and internal nodes are placed at the
most likely time of divergence.
.
TreeTime aims at striking a compromise between sophisticated
probabilistic models of evolution and fast heuristics. It implements GTR
models of ancestral inference and branch length optimization, but takes
the tree topology as given. To optimize the likelihood of time-scaled
phylogenies, treetime uses an iterative approach that first infers
ancestral sequences given the branch length of the tree, then optimizes
the positions of unconstraine d nodes on the time axis, and then repeats
this cycle. The only topology optimization are (optional) resolution of
polytomies in a way that is most (approximately) consistent with the
sampling time constraints on the tree. The package is designed to be
used as a stand-alone tool or as a library used in larger phylogenetic
analysis workflows.
.
Features
* ancestral sequence reconstruction (marginal and joint maximum
likelihood)
* molecular clock tree inference (marginal and joint maximum
likelihood)
* inference of GTR models
* rerooting to obtain best root-to-tip regression
* auto-correlated relaxed molecular clock (with normal prior)
Remark: This package will be maintained by the Debian Med team at
https://anonscm.debian.org/git/debian-med/python-treetime.git
--- End Message ---
--- Begin Message ---
Source: python-treetime
Source-Version: 0.0+20170607-1
We believe that the bug you reported is fixed in the latest version of
python-treetime, which is due to be installed in the Debian FTP archive.
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 864...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated python-treetime 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 14 Jun 2017 17:20:26 +0200
Source: python-treetime
Binary: python-treetime python-treetime-examples
Architecture: source all
Version: 0.0+20170607-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
python-treetime - inference of time stamped phylogenies and ancestral
reconstructio
python-treetime-examples - inference of time stamped phylogenies and ancestral
reconstructio
Closes: 864823
Changes:
python-treetime (0.0+20170607-1) unstable; urgency=medium
.
* Initial release (Closes: #864823)
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