bad phylip format

[Laurent Guéguen]

Hello,

I have a problem with the phylip alignments produced by bppseqman. 
With them I can not use seaview nor phyml, and apparently it is a problem
with the spaces before the sequences that are not recognized.
 
With codonphyml, the message is

  . One or more missing sequences in block 1.

And with seaview it is a bad format error.

Thanks,
Laurent

[Julien Yann Dutheil]

Hi Laurent,

I recently used seqman together with codonphyml without problem, i will check my option files... Maybe look at the interleaved vs sequential option, both in seqman and phyml? Phyml needs the "extended" version of phylip.
For Seaview, i think it only reads the "classic" phylip format.

Julien.

[Laurent Guéguen]

Hi Julien,

indeed with extended interleaved phylip, phyml is happy.

Thanks,
L

[Julien Yann Dutheil]

Hi Laurent,

I have checked my options: I used extented sequential for (codon)phyml. Phyml takes both sequential and interleaved, there is an option for that. But in any case it uses the "extended" format of PAML, not the original format of Phylip (that is, names of arbitrary length but separated by at least two space characters from the sequence content).

Cheers,

J.