[Biopython] Sequence alignment with multiple proteins

[Fahy, Michael]

This is not strictly a BioPython question but I'm using BioPython for
the work.

 

I have a set of 45 proteins and 10 species.  I have a  representative
orthologous protein from each set for each of the 10 species.  I'm
trying to build a phylogenetic tree by aligning the data from the 10
species.  I've tried concatenating the 45 protein sequences for each of
the 10 species and aligning the concatenated sequences but this has
produced results that do not make sense.  What do you recommend for such
a problem?

 

-------------------------------------------------------

Michael A. Fahy, PhD

Professor and Chair

Mathematics and Computer Science 

Chapman University

One University Drive

Orange, CA  92866

(714) 997-6879

fahy at chapman.edu