[EMBOSS] Notes about emma

[pmr at ebi.ac.uk]

Hi Aengus,

> Some queries about emma
>
> Though at the command line
> emma -osformat clustal
> or
> emma -osformat2 clustal
> or
> emma -osf clustal
> seem to work just as well.
>
> -osformat2 seems to be a red herring?

All these names are valid.

EMBOSS accepts any unambiguous short qualifier names, so -osformat can
naturally be reduced to -osf. The '2' is to allow several -osformat
associated qualifiers to have unique names. Without the '2' -osformat
refers to the current outseq, or to all outseqs.

> Slightly more worrying is the clustal format header which the above
> commands put in the .aln file
>
> CLUSTAL W(1.4) multiple sequence alignment

EMBOSS rewrites the ALN file as a general ALN format. The version number
is part of the EMBOSS 'clustal' format specification, and has no relation
to the clustal version used by emma.

Hope this helps,

Peter