Web lists-archives.com

Bug#864823: ITP: python-treetime -- inference of time stamped phylogenies and ancestral reconstruction




Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@xxxxxxxxxx>

* 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