Joseph W. Brown

Good start with 507ba5655ddbf3121432c0a616aa6dc93c53612e. Currently works with newicks with support as floats (`TEST/collapse.tre`). Handling integer support values should be straightforward.

91f68445422bd0624cddc9b0bab7866e1e727480 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...

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

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

That would be a great headstart! I had never heard of vcf before writing the existing function...

Hey @sprocha. Sorry this has not been addressed. Hopefully you've been able to accomplish this in some other way. Do you happen to have: 1. example input 2. expected output...

This is more general: phylip fails when piped to one of the alignments converts (pxs2*) as well. In this latter case, only 1 (the first) sequence is recognized and written...

Gah I am stumped on this one... For the moment try to avoid piping phylip format (the only one that seems to behave different in a file vs. a stream)....

Ok. The culprit indeed appears to be `is_complicated_phylip` (the function which tries to determine which (_of a plethora of_) format flavours is involved) i.e., when I comment this out (on...

72b4fa656c9c58ea5bf85fca9414d0694ae1689d better recognizes truly ultrametric trees. Likelihoods and parameter estimates from `pxbdfit` are _slightly_ off from that of `ape` (at fourth decimal place). Not sure if this is a further...