python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
Description
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)
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Homepage
https://github.com/neherlab/treetime
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