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Published September 13, 2021 | Version 1.5.0
Software Open

ms609/TreeTools: v1.5.0

Authors/Creators

  • 1. Department of Earth Sciences, Durham University

Description

New functions
  • ConstrainedNJ() returns an approximation to a neighbour-joining tree that respects constraints.
  • PolarizeSplits() marks a specified taxon as representing the ingroup of all splits.
  • Add KeepTip() and improve performance of DropTip().
  • ImposeConstraint() makes a tree consistent with topological constraints.
  • as.phylo.Splits() represents a Splits object as a tree.
  • Consensus() is a faster C++ implementation of ape::consensus().
  • ClusterTable() C++ functionality imported from "TreeDist".
Improved functions
  • Warn when empty cells passed to MatrixToPhyDat().
  • Warn when LabelSplits(labels) lack names.
  • SplitFrequency() drops tips from forest that aren't in reference.
  • AddTipEverywhere() supports trees with < 3 leaves.
  • Make RootTree() and PhyDatToMatrix() more robust.
  • Read[Tnt]AsPhyDat() passes additional parameters to Read[Tnt]Characters().
  • Support encoding option in ReadCharacters() function family.
  • Support CHARSTATELABELS in ReadCharacters().
  • Support for more formatting quirks in ReadNotes().
  • Better support ambiguous tokens in WriteTntCharacters().
Optimization
  • Fast matching functions from "fastmatch".
  • Improve efficiency of Preorder() and Postorder(), and lift limit on tree size.

Files

ms609/TreeTools-1.5.0.zip

Files (909.9 kB)

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md5:96e51166c4f3b9702ad7734daa1ad8c2
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Additional details

Related works

Is supplement to
https://github.com/ms609/TreeTools/tree/1.5.0 (URL)