program to Reformat sequences?

Bernard Murray, PhD spam at
Mon Nov 15 02:16:57 EST 1999

In article <705E975A40BED211949800105A1C2F4C54CC83 at sailfish.hboi.edu>,
lopez at HBOI.edu (Jose Lopez) wrote:

> Dear ColleaguesI am looking for a program (preferably shareware)
> that can reformat FASTA
> blocks or interleavedDNA sequence alignments (txt files) into triplet
> (codons) form, and which
> preserves the alignments.  If the programcan convert between other
> formats (GCG, MEGA etc) , even better!I would appreciate any leads.
> Cheers Jose V. Lopez, Ph.D.

I have a (rather crude) Perl script that will take a Clustal-style
alignment file and split it into individual sequences (keeping the gaps).
If it is of any help then use the (modified) address below to contact me.
It works with Linux and DOS (DJGPP).  I haven't tried MacPerl (yet).

I'm not sure what you want with the triplets as unless it is an
obvious ORF the reading frame would be arbitrary and gaps would
screw up frames in individual sequences.


Bernard P. Murray, PhD
bpmurray at cgl . ucsf . edu
Department of Cellular & Molecular Pharmacology, UCSF

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