Using -bf option with terminal branches fails, terminal branches are always ignored
Would be good to make -bf option works for terminal branches. And also to allow all terminal branch computations (maybe not by default! => new option?)
FROM https://rt.isb-sib.ch/Ticket/Display.html?id=101927
Dear Xiaofan Zhou,
You're indeed right that FastCodeML is designed to test only internal branches. This was an early decision that was made during the implementation of the software.
We are working on a new version that will remove such constrains and we are hoping to release it as soon as possible.
Best,
Nicolas
Dear Selectome Staff,
I am writing to ask for your help with the software FastCodeML. I wanted to use it for branch-site test of positive selection on all branches in a phylogenetic tree. However, it seems to me that FastCodeML only performs such test on internal branches of the tree. For example, if I don’t specify any foreground branch (i.e. no “-bf” option), FastCodeML would iterate through all internal branches. If I enable the “-bf” option with a terminal branch labeled in the tree, FastCodeML would ignore the user-specified foreground and behave just like the “-bf” option is off. I am wondering if FastCodeML is designed for internal branches only, or am I missing something? Could you please let me know if there is a way to run FastCodeML on all branches? Thanks very much!
Best,
Xiaofan Zhou