Dear Robin,
Starting with release 6.2 the program needleall is included into the EMBOSS
software package. This program allows the generation of all vs. all alignments
of two sequence sets. So you can generate all alignments with just one program.
See http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/needleall.html
for more information.
The best thing about needleall is you do not need to write a Perl script, no
matter if this is just a simple script.
Maybe this can help you to find arguments for upgrading to a newer EMBOSS
release.
Best regards,
Frank
--
Dr. rer. net. Dipl. Biochem. Frank Förster
Department of Bioinformatics
University of Würzburg, Germany
Fon: +49 931 - 31 84555
Fax: +49 931 - 31 84552
frank.foers...@biozentrum.uni-wuerzburg.de
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