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

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