matsen/pplacer — Issue #234: guppy fat sets many branch lengths to 0.01
Author: joelb123
Created: 2012-02-29 18:17:41+00:00
State: open

Hi,

Thanks for writing pplacer. I'm enjoying using it thus far.

My version is pplacer-v1.1.alpha11rc1-Linux-2.6.32. I'm using it under Gentoo linux. Everything is highly up-to-date. I did not build from source.

It seems that guppy fat messes with branch lengths. It's my understanding from the pplacer paper that "pplacer placements all sit on a single reference tree with associated branch lengths fixed". Yet the branch lengths from guppy fat are not the same as in the input tree. In particular, the really fat branches get set to exactly 0.01 for my tree:

$ xml_grep branch_length guppy_fat_tree.phyloxml |grep 0.01\<

0.01
...20 more examples suppressed..

Presumably this was done for some reason involving readability, but it has the effect of obscuring the effects one is looking for. Is it easily switched off?