[EMBOSS] seqret options

[Peter Rice]

Derek Gatherer wrote:

> Dear EMBOSSers
> 
> I'm trying to write a pipeline to take a load of paired, aligned 
> homologues from 2 species and submit them sequentially to the yn00 
> application from the well known PAML package.  PAML's applications all 
> take PHYLIP format.

> Failing that, PAML takes the other, non-interleaved phylip format 
> ("sequential") by default, and that would not require any flag 
> insertion. 

Last time I worked through the PHYLIP formats (for EMBOSS 2.10.0) I found 
Phylip had changed the format it used.

One change was that I removed the YF from phylip3 format because phylip was no 
longer using it - so updating to EMBOSS 2.10.0 will solve your non-interleaved 
format problem (and David Bauer's code fix is exactly what you need).

Any more feedback on the variations of phylip formats that other packages use 
would be a great help!

We will be releasing the PHYLIP 3.6 integration (as a PHYLIPNEW EMBASSY 
package) soon and expect to see more use of phylogenetics packages with EMBOSS.

regards,

Peter Rice