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python-treetime_0.0+20170607-1_amd64.changes (click to toggle)
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-packaging@lists.alioth.debian.org>
Changed-By:Andreas Tille <tille@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)
Files:
2d9cdf56fdfc685191b8e0ee68590f1e 2162 science optional python-treetime_0.0+20170607-1.dsc
0b62f33e1eab7886a42d55d779241f2a 143624 science optional python-treetime_0.0+20170607.orig.tar.xz
d304646d183a78eb813f250536c3c9a0 5264 science optional python-treetime_0.0+20170607-1.debian.tar.xz
60c6df415f90a55e8452aca26b7f3538 217010 python optional python-treetime-examples_0.0+20170607-1_all.deb
f0115829d51e9929ea1c1ae57954eb08 59060 python optional python-treetime_0.0+20170607-1_all.deb
0e699d0b961f3530ba324f71f054d733 5620 science optional python-treetime_0.0+20170607-1_amd64.buildinfo
python-treetime_0.0+20170607-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:python-treetime
Binary:python-treetime, python-treetime-examples
Architecture:all
Version:0.0+20170607-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Andreas Tille <tille@debian.org>
Homepage:https://github.com/neherlab/treetime
Standards-Version:3.9.8
Vcs-Browser:https://anonscm.debian.org/cgit/debian-med/python-treetime.git
Vcs-Git:https://anonscm.debian.org/git/debian-med/python-treetime.git
Build-Depends:debhelper (>=10), dh-python, python-all, python-setuptools
Package-List:python-treetime deb python optional arch=all python-treetime-examples deb python optional arch=all
Files:
0b62f33e1eab7886a42d55d779241f2a 143624 python-treetime_0.0+20170607.orig.tar.xz
d304646d183a78eb813f250536c3c9a0 5264 python-treetime_0.0+20170607-1.debian.tar.xz
lintian check for python-treetime_0.0+20170607-1.dsc (click to toggle)
README.source for python-treetime_0.0+20170607-1.dsc (click to toggle)
No README.source in this package
control file for python-treetime_0.0+20170607-1_all.deb (click to toggle)
Package:python-treetime
Version:0.0+20170607-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:282
Depends:python:any (<<2.8), python:any (>=2.7.5-5~), python-numpy, python-scipy, python-biopython, python-pandas
Section:python
Priority:optional
Homepage:https://github.com/neherlab/treetime
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)
lintian check for python-treetime_0.0+20170607-1_all.deb (click to toggle)
contents of python-treetime_0.0+20170607-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2017-06-14 15:20 ./
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/bin/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/lib/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/lib/python2.7/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/
-rw-r--r-- root/root       177 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/__init__.py
-rw-r--r-- root/root     16183 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/aa_models.py
-rw-r--r-- root/root      4497 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/branch_len_interpolator.py
-rw-r--r-- root/root     30810 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/clock_tree.py
-rw-r--r-- root/root       408 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/config.py
-rw-r--r-- root/root     13287 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/distribution.py
-rw-r--r-- root/root     26374 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/gtr.py
-rw-r--r-- root/root      2952 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/io.py
-rw-r--r-- root/root     11888 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/merger_models.py
-rw-r--r-- root/root      9838 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/node_interpolator.py
-rw-r--r-- root/root      6891 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/nuc_models.py
-rw-r--r-- root/root     11641 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/seq_utils.py
-rw-r--r-- root/root     50124 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/treeanc.py
-rw-r--r-- root/root     33686 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/treetime.py
-rw-r--r-- root/root      5125 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime/utils.py
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime-0.1.1.egg-info/
-rw-r--r-- root/root       427 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime-0.1.1.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime-0.1.1.egg-info/dependency_links.txt
-rw-r--r-- root/root         9 2017-06-14 15:20 ./usr/lib/python2.7/dist-packages/treetime-0.1.1.egg-info/top_level.txt
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/doc/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/doc/python-treetime/
-rw-r--r-- root/root       165 2017-06-14 15:20 ./usr/share/doc/python-treetime/changelog.Debian.gz
-rw-r--r-- root/root      1400 2017-06-14 15:20 ./usr/share/doc/python-treetime/copyright
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/doc/python-treetime/examples/
-rw-r--r-- root/root      1894 2017-03-06 10:55 ./usr/share/doc/python-treetime/examples/ancestral_inference.py
-rw-r--r-- root/root      3050 2017-06-02 16:38 ./usr/share/doc/python-treetime/examples/ebola.py
-rw-r--r-- root/root      2693 2017-01-01 18:09 ./usr/share/doc/python-treetime/examples/relaxed_clock.py
-rw-r--r-- root/root      3368 2017-06-02 16:38 ./usr/share/doc/python-treetime/examples/rerooting_and_timetrees.py
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/man/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/man/man1/
-rw-r--r-- root/root       638 2017-06-14 15:20 ./usr/share/man/man1/ancestral_reconstruction.1.gz
-rw-r--r-- root/root       699 2017-06-14 15:20 ./usr/share/man/man1/temporal_signal.1.gz
-rw-r--r-- root/root      1060 2017-06-14 15:20 ./usr/share/man/man1/timetree_inference.1.gz
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/treetime/
-rwxr-xr-x root/root      3059 2016-12-22 10:03 ./usr/share/treetime/ancestral_reconstruction.py
-rwxr-xr-x root/root      4101 2016-12-23 08:56 ./usr/share/treetime/temporal_signal.py
-rwxr-xr-x root/root      5567 2016-12-22 10:03 ./usr/share/treetime/timetree_inference.py
lrwxrwxrwx root/root         0 2017-06-14 15:20 ./usr/bin/ancestral_reconstruction -> ../share/treetime/ancestral_reconstruction.py
lrwxrwxrwx root/root         0 2017-06-14 15:20 ./usr/bin/temporal_signal -> ../share/treetime/temporal_signal.py
lrwxrwxrwx root/root         0 2017-06-14 15:20 ./usr/bin/timetree_inference -> ../share/treetime/timetree_inference.py
control file for python-treetime-examples_0.0+20170607-1_all.deb (click to toggle)
Package:python-treetime-examples
Source:python-treetime
Version:0.0+20170607-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:280
Depends:python-treetime
Section:python
Priority:optional
Homepage:https://github.com/neherlab/treetime
Description:
inference of time stamped phylogenies and ancestral reconstruction (example)
 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)
 .
 This package contains example scripts and data to test the usage of
 treetime.
lintian check for python-treetime-examples_0.0+20170607-1_all.deb (click to toggle)
contents of python-treetime-examples_0.0+20170607-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2017-06-14 15:20 ./
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/doc/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/doc/python-treetime/
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/doc/python-treetime/data/
-rw-r--r-- root/root      2052 2015-10-06 16:00 ./usr/share/doc/python-treetime/data/H3N2_NA_allyears_NA.20.fasta.gz
-rw-r--r-- root/root      1455 2016-01-19 14:33 ./usr/share/doc/python-treetime/data/H3N2_NA_allyears_NA.20.metadata.csv
-rw-r--r-- root/root      1567 2015-10-06 16:00 ./usr/share/doc/python-treetime/data/H3N2_NA_allyears_NA.20.nwk
-rw-r--r-- root/root     13769 2015-10-06 16:00 ./usr/share/doc/python-treetime/data/H3N2_NA_allyears_NA.200.fasta.gz
-rw-r--r-- root/root      4708 2016-04-04 11:59 ./usr/share/doc/python-treetime/data/H3N2_NA_allyears_NA.200.metadata.csv.gz
-rw-r--r-- root/root      4662 2015-10-06 16:00 ./usr/share/doc/python-treetime/data/H3N2_NA_allyears_NA.200.nwk.gz
-rw-r--r-- root/root     30810 2015-10-06 16:00 ./usr/share/doc/python-treetime/data/H3N2_NA_allyears_NA.500.fasta.gz
-rw-r--r-- root/root      9725 2015-10-06 16:00 ./usr/share/doc/python-treetime/data/H3N2_NA_allyears_NA.500.nwk.gz
-rw-r--r-- root/root         0 2015-03-31 10:35 ./usr/share/doc/python-treetime/data/__init__.py
-rw-r--r-- root/root      2446 2016-12-22 14:16 ./usr/share/doc/python-treetime/data/ebola.csv.gz
-rw-r--r-- root/root    180472 2016-12-22 14:16 ./usr/share/doc/python-treetime/data/ebola.fasta.gz
-rw-r--r-- root/root      6133 2016-12-22 14:16 ./usr/share/doc/python-treetime/data/ebola.nwk.gz
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/doc/python-treetime/test/
-rw-r--r-- root/root        81 2015-04-02 15:51 ./usr/share/doc/python-treetime/test/__init__.py
-rw-r--r-- root/root      1816 2017-06-14 15:20 ./usr/share/doc/python-treetime/test/test_gtr.py
-rw-r--r-- root/root       556 2015-11-25 11:02 ./usr/share/doc/python-treetime/test/test_seq2prof.py
-rw-r--r-- root/root      3243 2017-06-05 12:46 ./usr/share/doc/python-treetime/test/test_treetime.py.gz
-rw-r--r-- root/root      1181 2017-06-14 15:20 ./usr/share/doc/python-treetime/test/tree_time_test.py
drwxr-xr-x root/root         0 2017-06-14 15:20 ./usr/share/doc/python-treetime-examples/
-rw-r--r-- root/root       165 2017-06-14 15:20 ./usr/share/doc/python-treetime-examples/changelog.Debian.gz
-rw-r--r-- root/root      1400 2017-06-14 15:20 ./usr/share/doc/python-treetime-examples/copyright

Timestamp: 15.06.2017 / 14:01:07 (UTC)