raxml and constraining sister taxa to monophyletic group to be used as an outgroup

[SuzanaS]

Dear all,

I would like to use several bacterial sequences for rooting a mitochondrial tree. However, raxml reports warning that the outgroup is not monophyletic. This even when only two bact. sequences from the same family are specified and I am not sure what is a good approach.

Would it be possible to constrain bact. sequences to one group and then specify it as an out-group in the call for rapid bootstrapping? 

I would like to test how clustering looks when the outgroup is specified in the initial ML search and bootstraping.

Thank you much in advance!

Suzana

[Alexandros Stamatakis]

Hi Suzana,

I think the best solution would really be to use the evolutionary
placement algorithm for assessing the reliability of outgroup placements
on the ingroup phylogeny (please see related posts about this on this
google group).

Just constraining the outgroup taxa to be monophyletic, i.e., to force
them together, introduces a bias I think.

Alexis

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[SuzanaS]

Hi Aleksis,

Thank you much for a fast reply and advice! Just found the EPA paper and will look trough the posts too. 

Suzana