Program that collapses poorly supported edges

[josephwb]

Pretty simple, but very useful!

User will provide a tree file and a minimum threshold: any edge with support < threshold gets collapsed.

[josephwb]

Possible option: if tree is ultrametric (i.e., a chronogram) deal with edge lengths to preserve ultrametricity.

(Whenever I read "ultrametricity" (am I the only one who uses this word?) I automatically hear Will Ferrell's voice)

[josephwb]

Hmm this is a bit trickier than at first sight. Specifically: there are 1) a tons of formats (e.g. annotated Nexus files like from FigTree vs. plain newick), and 2) support ranges (percentage vs. proportion).

For first stab, will expect simple proportion node labels: )0.4

[josephwb]

Good start with 507ba56. Currently works with newicks with support as floats (TEST/collapse.tre). Handling integer support values should be straightforward.

[josephwb]

91f6844 handles trees with either proportions or percentages for support values (guesses the scale by the first one encountered). Part of this involved the decision to force the threshold passed in to be a proportion. If the tree itself has percentages, this should be detected. The point of this 'guessing' is to allow a default threshold of 0.5 support (which may be typical).

Parsing Nexus node annotations will be next.

[josephwb]

Ack, this is another that got forgotten. Looks like this got pretty far. Will look into this more tomorrow.

[josephwb]

The only thing remaining here is the processing of annotated nexus files e.g. those produced by figtree/treeannotator.