Phylogenetics

Phylogenetics with the Wolfram Language.

Related post at Mathematica.StackExchange: How to work with phylogenetic trees? http://mathematica.stackexchange.com/q/126496/89

Description

The Phylogenetics` package can:

• parse a Newick tree string to a Mathematica-usable Tree object and write a Tree object to a Newick string;
• parse a Cluster object of the HierarchicalClustering` package to a Tree and convert a Tree to Cluster representation;
• test properties of Tree objects;
• extract vertices, edges, internal nodes, leafs, sub- and supertrees of Tree objects;
• directly calculate various properties of Tree objects like paths and distances between vertices;
• convert a Tree object to Graph, and a tree Graph to Tree; any tree graph (TreeGraph, ClusteringTree, etc.) for which TreeGraphQ returns True can be converted to Tree;
• convert a Tree object or a Graph tree to Cladogram graph,
• provide example trees in Newick and Cluster format.

Version history

• 2016 09 08: Package initialized.
• 2016 09 16: PUBLISHED: Version 1.0.0.
• 2016 01 31: PUBLISHED: Version 1.1.0.
  • ADDED: CommonAncestor, DivergenceTime, AncestorIndex, TreeDistanceMatrix, TreeTop, $PhylogeneticsVersionNumber.
  • FIXED: Usage message corrections.
  • FEATURE: Straight Cladogram edges, branching according to angle.
  • MODIFIED: LeafQ and NodeQ now can be applied to a single argument representing a node association.
  • RENAMED: SubnodeIndex to DescendantIndex.
  • MODIFIED: Code was made compatible down to Mathematica 10.0. No compatibility before that due to heavy usage of associations.

Sources

• The Newick Standard: http://evolution.genetics.washington.edu/phylip/newicktree.html
• Wikipedia: Newick format: https://en.wikipedia.org/wiki/Newick_format
• Newick tree formats: http://marvin.cs.uidaho.edu/Teaching/CS515/newickFormat.html
• An online Newick tree visualizer: http://etetoolkit.org/treeview/
• Parfrey, Lahr, Knoll & Katz 2011: Estimating the timing of early eukaryotic diversification with multigene molecular clocks. PNAS 108, 13624 - 13629. doi: http://dx.doi.org/10.1073/pnas.1110633108. Supplementary Information.

By István Zachar 2016-2017