[Bioperl-l] How to determine strains were evolved independently in a phylogenetic tree?

[longbow leo]

Hi,

I have created a phylogenetic for a virus protein which contained about 200
strains. Next I need to do an analysis to check whether several strains in
this tree were evolved independently. Although it is not too difficult to do
manually, I still have litter idea how to do this in a Perl script since
there are some datasets need to do.

At first I tried to use the method "is_monophyletic" in the module
"Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
work as I have thought. According to the description of "is_monophyletic"
method, it "Will do a test of monophyly for the nodes specified in
comparison to a chosen outgroup". Does here test whether the outgroup strain
is monophyletic to the nodes, or test the nodes only? The description sounds
like the latter but the what the script did seemed to be the first.

Are there any suggestions?

Thank you very much!


Haizhou Liu