#52 Support for Phyml and RAxML sequence formats
Markus Göker wrote:
> Not as a further bug report, but as a request for an additional sequence
> format, I would like to ask whether you could include the format used by
> Phyml and RAxML in the next EMBOSS release. Both programs, particularly
> RAxML (http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm), which
> is the fastest maximum likelihood program available, are used by an
> increasing number of researchers.
>
> The format is easy and quite close to PHYLIP format, except for the
> following features:
>
> * Sequence labels can be longer than 10 characters;
>
> * Sequence labels must not contain whitespace;
>
> * Whitespace (a newline also works) must separate the sequence label
> from the first nucleotide or amino acid;
>
> * For use with RAxML, sequences must not be interleaved.
>
> In the case you're interested, to illustrate this "extended PHYLIP
> format" or "EPF" I've attached a small example file.
Thanks. We will add it, but it may not be one we can allow by default so
you may have to put -sf phyml on the command line.
We need to check that it does not conflict with any other formats that
start with two numbers. The coding part is easy.
regards,
Peter Rice
