[Bioperl-l] Phylip format error

[Fields, Christopher J]

Alexey,

Just want to point out that 'relaxed phylip' format was introduced long after this parser was created; in fact (as Adam points out) there was an alternative workaround to deal with the lossy names.  

The content of that page is on a wiki, which anyone is free to edit (just need an OpenID to set up an account).

chris

On May 23, 2013, at 2:22 AM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
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