[Biopython] Biopython function for operating multiple homologous sequences in a single file

[Edson Ishengoma]

Hi all,

I have a single large file containing many (thousands) coding sequence
pairs according to their homologs as so:

> >ENSBTAT00000048342_species1
> sequences
> >ENSBTAT00000048342_species2
> sequences
> >ENSBTAT00000009085_species1
> sequences
> >ENSBTAT00000009085_species2
> sequences
> >ENSBTAT00000009212_species1
> sequences
> >ENSBTAT00000009212_species2
> sequences
> ......
> ......
> ......
>

Now I want to produce a clustalw alignment for each cds pair. Is there a
way to use the biopython commandline function for clustalw to treat each
gene pair separately for all pairs, run alignment and produce an ouput
(alignments + trees file)?

I appreciate your time and look forward to hear from you,

With regards,

Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
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*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
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<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

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