[EMBOSS] emma doest not work for nucleic sequences

[Duhaime Johanne]

Hello

emma works fine with clustawl 1.83 but not with 1.82 or 2.0. Thank you very much!

Johanne
-----Message d'origine-----
De : Peter Rice [mailto:pmr at ebi.ac.uk]
Envoyé : Wednesday, 16 April 2008 11:23
À : Duhaime Johanne
Cc : emboss-bug at emboss.open-bio.org
Objet : Re: [EMBOSS] emma doest not work for nucleic sequences

Duhaime Johanne wrote:
> Hello
>
> I installed version 5 of Emboss on Solaris 9. I compiled a 64 bits version. When I run emma with a protein file it work fine. But when I use nucleic sequences it does not. Clustawl, by itself, work fine with nucleic sequences.
>
> Emma  (protein)
> Multiple alignment program - interface to ClustalW program
> Input (gapped) sequence(s): multipleprotein.tfa
> output sequence set [hs70_achkl.aln]:
> Dendrogram (tree file) from clustalw output file [hs70_achkl.dnd]:
>
>  CLUSTAL W 2.0 Multiple Sequence Alignments
> Sequence type explicitly set to Protein
> Sequence format is Pearson
> number of seqs is: 5
> (...)
>
> Emma (nucleic)
> Multiple alignment program - interface to ClustalW program
> Input (gapped) sequence(s): multiplenucleic.tfa
> output sequence set [ai632122.aln]:
> Dendrogram (tree file) from clustalw output file [ai632122.dnd]:
>
>  CLUSTAL W 2.0 Multiple Sequence Alignments
>
> Error: parameter required for /dnamatrix

Ah, so you are using clustalw 2.0

Emma was designed for clustalw 1.83

Perhaps we need to look at the differences between clustal versions and
provide some extra logic in emma (we will try to avoid running two
different 'emma's)

regards,

Peter