[EMBOSS] using emma: where to put clustalw

Robin Colgrove robin at hms.harvard.edu
Tue Apr 12 14:17:42 UTC 2005


I was trying to use emma for a multiple sequence alignment of dna 
sequencing reads, but it complained that it could not find clustalw. I 
could not find any mention of clustalw on the EMBOSS page, so I got a 
copy from the clustalw homepage and -not knowing where to place it- 
tried the /usr/local/share/ EMBOSS/acd directory. That didn't work, and 
emma gives the error:

    EMBOSS An error in ajsys.c at line 398:
cannot find program 'clustalw'

Looking in the emma.acd and ajsys.c files, I can't find any guidance.

Does anyone know how this is supposed to work?
Alternatively, is there another good way to do multiple sequence 
Looking ahead, I do not find any obvious way to do contig assembly, a 
la Phrap, or CAP.


robin colgrove

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