A toolkit for working with phylogenetic data.
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Labelled Tree

Summary

Takes a jplace file and optionally a Newick tree (for example, with additional bootstrap support values) and produces a Newick tree where each Placement is turned into an individual branch on the original tree.

This demo is located at

genesis/doc/demos/labelled_tree.cpp

Details

The program takes either two or three arguments:

./labelled_tree <jplace_file> [<newick_tree_file>] <output_newick_tree_file>

It then produces a labelled tree for the given jplace Sample. That is, the resulting tree contains a leaf node for each Placement of the Sample. See labelled_tree() for details.

If the optional <newick_tree_file> is given, this tree is used instead of the tree contained in the jplace file. It has to be topologically identical to the jplace tree, but can contain additional values like bootstrap support values. Currently, we only support such values that are stored as inner node names. This is for example given if a bootstrap tree of RAxML is used. When working with trees containing such values at inner nodes, also be aware of issues that might arise with other programs. See https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msx055 for details.

In the beginning of the main function of the program, there are two settings fully_resolve and name_prefix, according to the two optional arguments of labelled_tree(), that can be changed if needed.