Dear Sergei,

I'm trying to determine in a tree if one branch has a significant relative branch length compared to the other branches on the same tree.
I just started HyPhy and have no experience in it whatsoever, what I do know is that it’s possible somehow to compare two branches in the tree. Thus, a possible way for my problem would be to perform multiple pairwise comparisons to determine the branch that has a higher relative branch length compared to all the others. But is there a more direct way to do it without iterating the program on each pairwise comparison?

Hopefully you can help me…if you need more detail, please let me know …

Thanks a million,

Nora

Dear Nora,

I want to make sure I understand you correctly. You wish to test if a particular branch in the tree is longer than the rest of the branches (e.g. measured by their average, or their maximum)? There is no pre-written test for this in HyPhy, but it's not difficult to write, and I have similar files floating around in my archives. Let me see if I can dig them out.

Cheers,
Sergei

Hi Sergei,

yes that's about it. If you do have files floating around I'll be very happy to have one.

Thanks,

Nora

Dear Nora,

Try Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login (you need the latest HyPhy build to run it). It'll let you select a branch to test and compare it to

1). Every other branch (using multiple test corrections), i.e. return all those branches which are significantly shorter than the foreground.
2). The mean of the rest of the branches, i.e. whether the foreground is longer than average
3). The maximum of the rest of the branches, i.e. whether the foreground is the longest

You can do nuc/protein/codon tests, and also check for either full branch lengths (global models) or portions of branch lengths (e.g. only synonymous lengths, using a local version of a codon model and constraining synRate) etc.

Cheers,
Sergei