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

Gregory Jordan greg at ebi.ac.uk
Thu Sep 8 06:40:30 EDT 2011


Hi Haizhou,

I'm not sure I understand exactly what you're trying to do. But to clarify
the BioPerl code: the is_monophyletic method (for the actual code, see here
https://github.com/bioperl/bioperl-live/blob/master/Bio/Tree/TreeFunctionsI.pm#L832)
tests
whether the single outgroup node falls *within* or *outside* the last common
ancestor of the group of nodes given. If the outgroup node falls *outside*
the subtree defined by this LCA node, then the group of nodes can be called
monophyletic with respect to that outgroup (at least as far as my
understanding of the word 'monophyletic' goes). If the outgroup node falls
*within* the subtree defined by this LCA node, then the group of nodes is
not monophyletic with respect to that outgroup node.

The term "evolved independently" sounds slightly vague to me -- what is it
exactly about the shape of your tree that allows you to call a strain
independent or not? If you gave an example or two of trees where you
consider the evolution to be independent and non-independent, I (or someone
else on the list) may be able to help you find the right method to do this
automatically.

Cheers,
 Greg

On Wed, Sep 7, 2011 at 9:19 PM, longbow leo <longbow0 at gmail.com> wrote:

> 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
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