Option to not label MRCA with label-tree.bf

[hverdonk]

I want to perform RELAX and Contrast-FEL analyses on highly diverged dengue serotypes. The serotypes themselves cluster nicely, but there are long branches separating the clades that I don't want to include in my comparative analysis.

I used label-tree.bf to label each clade using regular expressions, but the long branches leading to the most recent common ancestor of each clade are also labeled. I would like an option to ignore the MRCA when labeling internal nodes.

[hverdonk]

@spond

[spond]

Dear @hverdonk,

Try the --internal-nodes "All descendants, no MRCA" option in the just updated label-tree.bf. It may be too aggressive, so check. I should work well on the trees where you don't have a particular labeled clade spanning the root.

Best,
Sergei

[hverdonk]

This works very well for three of my clades (DENV2, DENV3, and DENV4), but some of the internal branches in DENV1 should be tagged but are not tagged. I believe that one of the nodes in DENV1 was likely chosen (arbitrarily) as the root. I've attached one of the newick trees I labeled as an example.

nonstructural_protein_NS3-nodups.DENV4.txt