[EMBOSS] seqret options

[Derek Gatherer]

I do have 2.10.0:

[gath01d at gamma seqs]$ seqret -osformat phylip3 barf1_both.seq
Reads and writes (returns) sequences
Output sequence [c-barf1.phylip3]: barf1.phylip3
[gath01d at gamma seqs]$ more barf1.phylip3
1 663 YF
c-barf1ATGGCCAGGC TTTTCGCTCA GCTGCTCCTG CTCGCGGGCT CCGTCGCCTC
           CTGCCTGGCC GTCACCGCCT TTGTGGGTGA GCGGGCCGTC CTGAGTTCCT
           ACTGGAAGAG GGTGAGCCTA GGGCCCGAGA TCATGGTGGA ATGGTTCAAA
[gath01d at gamma seqs]$ embossversion
Writes the current EMBOSS version number
2.10.0

Anyway, I know how to do the code fix now, so thanks to all.

Cheers
Derek

At 13:23 15/06/2005, you wrote:
>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
>