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Releases: matsengrp/gctree

v4.0.3

06 Jun 22:16
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What's Changed

Full Changelog: v4.0.2...v4.0.3

v4.0.2

18 May 21:10
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What's Changed

  • Simplify abundance logic and remove tuple sequence names by @willdumm in #89
  • Fix numpy errors on gctree import by @willdumm in #94

Full Changelog: v4.0.1...v4.0.2

v4.0.1

03 May 23:47
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New Contributors

Full Changelog: v4.0.0...v4.0.1

v4.0.0

01 Mar 03:23
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Summary

  • A major enhancement for parsimony tree search is the use of a history DAG to expand the set of trees found by dnapars, often by orders of magnitude. h/t @willdumm
  • Tree ranking can now use a linear combination of branching process likelihood, isotype parsimony, and mutability parsimony (e.g. from a 5mer context model) to score trees.

Backwards-incompatible changes

  • The CollapsedForest class no longer has a trees attribute, as the collection of trees is now represented as a history DAG.
  • The gctree CLI can now accept pickled parsimony forests from the current gctree version, but not from older versions.
  • Only the unique optimal tree is output by gctree infer, if it exists. If more than one tree is optimal, up to 10 will be output arbitrarily, and their numerical rankings will be arbitrary (rather than based on likelihood as before).

Pull requests

Full Changelog: v3.3.0...v4.0.0

v3.3.0

07 Jan 09:15
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Full Changelog: v3.2.1...v3.3.0

v3.2.1: Merge pull request #57 from matsengrp/56-disambiguate-optimally

03 Oct 02:49
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Patches a problem with resolution of ambiguous DNA characters in dnapars output.

h/t @willdumm

v3.2.0: Merge pull request #55 from matsengrp/render-options

13 Sep 23:59
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New API tree rendering options scale, branch_margin, and node_size described in docs.

v3.1.1: Merge pull request #54 from matsengrp/mlepatch

22 Aug 22:30
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Patches

  • Fixed a bug in empirical Bayes estimation of branching process parameters for CollapsedForest. Previous version v3.1.0 may have resulted in incorrect parsimony tree ranking
  • CollapsedTree.render() can now be used in a Jupyter notebook for tree visualization
  • Parameter checking for more flexible branching process simulations

v3.1.0

06 Aug 21:21
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New features

Developer notes

  • The branching_processes module has been refactored to remove illegitimate inheritance
  • Better default p, q parameters for MLE avoid gradient warnings.

v3.0.2

02 Jul 23:10
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Patch to set seeds for more repeatable behavior (especially in tests and docs), and better default rooting behavior for gctree infer.