[EMBOSS] using emma: where to put clustalw
Gary Williams, Tel 01223 494522
gwilliam at hgmp.mrc.ac.uk
Wed Apr 13 08:22:19 UTC 2005
Some alternate multiple alignment programs for nucleotide sequences on
the web are at:
I would recommend DIALIGN
Robin Colgrove wrote:
> Thanks to all for suggestions.
> Just putting clustalw in /usr/local/bin did the trick.
> Now, I need to figure out why emma/clustalw is giving me such bad
> Since I only had 4 sequences, I ended up aligning them pairwise with
> needle, then pieced together the full alignment in vi, but this is not
> going to fly as the number of sequences increases. The online tool I
> use for quick alignments (
> http://prodes.toulouse.inra.fr/multalin/multalin.html ) does fine, but
> the same fasta file sent either to emma or directly to clustalw gives
> obviously wrong alignments, even though the nucleotide sequences are
> highly homologous.
> thanks again
> On Apr 12, 2005, at 10:17 AM, Robin Colgrove wrote:
> > Hello.
> > 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
> > alignment?
> > Looking ahead, I do not find any obvious way to do contig assembly, a
> > la Phrap, or CAP.
> > thanks
> > robin colgrove
MRC Rosalind Franklin Centre for Genomics Research
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