[Chimera-users] Analysis of the multiple alignments + structures

[Elaine Meng]

Dear James,
This is beyond my expertise.  Note that Chimera does not calculate phylogenetic trees, it only displays them.

If you don’t get helpful responses from the Chimera list, maybe you can ask this question on some bioinformatics forum instead, or the authors of similar papers. Lacking direct knowledge, my best advice is always to search the literature and read papers that seem similar in some way to what you want to do.
Best,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 8, 2014, at 2:46 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Chimera users!
> 
> I've been interested in the possibility to make some sort of evolutional analysis in Chimera using MSA of the protein under study, its X-ray structures and its superimpositions as well as obtained projections of the sequence conservation in key (functionally-important) hot spots made by means of mutalign plugin. For my particular case I have MSA for the big number of olfactory receptors sequences (including receptors from different sub-groups associated with different specificity towards different odors). As the result I should to find possibility to  sort these sequences of each ORs based on some phylogenetic study (I thinks to obtain tree-like view of the sequences) considering explicitly residues of the receptor's binding site.  One of the possible idea is to keep only those residues of interest (from the ligand binding cavity) and rerun the alignment on these mini sequences to make prediction of new family of Or that may interact with the same kind of odorants. Would this idea is better realized by means of differential evolutional tracing method (because In fact we need to subtract conservative residues of one sub-branch of the whole phylogeny tree from those of all (root) OR) or there are any trivial alternatives? 
> 
> Thanks for help,
> James