Bug#864823: ITP: python-treetime -- inference of time stamped phylogenies and ancestral reconstruction
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@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
Reply to: