Hi all,

If anyone is interested, I've just wrapped a little Python script
I'd prepared early for use in Galaxy for a fairly common need -
"back translating" a protein alignment into a nucleotide alignment
by threading the unaligned sequence.

We're testing this locally, and barring any major issues I
would expect to release this to the main Tool Shed in a week
or so - but if any of you want to have a play with it now, and
pass on feedback, please do so:

Development repository:

Test Tool Shed release:

Planned Tool Shed release:
http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans (pending)

This uses Biopython's AlignIO [*] module and so can handle a
range of alignment file formats - for now I have restricted this
to "fasta", "clustal" and "phylip" which I believe are all already
in use on the tool shed - there is probably scope here for a
more coordinated effort to define Galaxy datatypes in this
area, including things like the PFAM/Stockholm format and
strict/relaxed variants of PHYLIP.



[*] http://biopython.org/wiki/AlignIO
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