[Bioperl-l] Phylip format error

[Alexey Morozov]

Which is also worsened by the fact that there is relaxed phylip format,
which allows up to 250 chars for taxon name. They are separated from a
sequence by single space, which creates problems if names were extended to
10 chars in strict Felsenstein's format by whitespaces. On the whole,
phylip is as messily defined format as one can make from a plain textfile
with information content of fasta.
Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
phylip and how does it tell dialects from one another. Even if code support
is OK, it may be worthwile to explain it somewhere at bioperl.org


2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>

> Hello!
>
> I happen to have checked to see what the PERL webpage says about Phylip
> format for DNA alignment files and see that it is erroneous.
>
> I am not a PERL user and do not want to be bothered to register or
> otherwise learn how to make an official comment, so forward this for
> someone to pick up.
>
> Phylip format allows up to 10 spaces for taxon names; the data must start
> in the 11th space. This can be checked on Jo Felsenstein's site.
>
> The PERL page accessed by searching for "Phylip format PERL" allows only 8
> spaces for the name.
>
> B. L. Cohen
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>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.