[Bioperl-l] Bio::SearchIO::amps and Bio::SearchIO::mrbayes_nexus

[Nathan Haigh]

I was under the impression that NEXUS format blocks should end with "end;"
(Maddison et al. 1997) and it was later that some software started using
"endblock" instead. Therefore, "end;" should be used for output, but for
backwards compatibility "endblock;" should also be handled correctly for
input - Although I haven't reread Maddison et al. 1997 to confirm this - no
searchable pdf either :o(

You may also find this page useful:
http://camel5.umbi.umd.edu/camel/projects/nexus/

They have a tool "NEXPL" which contains a pretty comprehensive nexus parser
which is able to handle quite a few different nexus blocks.

Also, after I contacted Fredrik Ronquist he said that after a period of
relatively slow progress they are accelerating the development of MrBayes
this year with the addition of three new people to the development team.
I've been told that Paul van der Mark (his new postdoc) is the person most
suitable to contact with suggestions etc (let me know if you want his e-mail
address). Hopefully MrBayes will be a little more NEXUS compliant than it
currently is.

Nathan

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Matthew Betts
Sent: 11 May 2005 12:54
To: BioPerl
Subject: [Bioperl-l] Bio::SearchIO::amps and Bio::SearchIO::mrbayes_nexus


Hi,

I was thinking of writing a Bio::SearchIO module for AMPS block format. 
This is the format used by alscript and stamp. Both of these come with 
format converters, but would be useful for me to do it within bioperl. OK 
for me to write Bio::SearchIO::amps, or is there something else already? 
Is that name OK?

Secondly, MrBayes doesn't like some things in the Nexus format output by 
Bio::SearchIO::nexus (the 'symbols' parameter, and it expects 'end;' 
rather than 'endblock;') even though they're valid nexus... OK to copy 
Bio::SearchIO::nexus to Bio::SearchIO::mrbayes_nexus and make the 
necessary changes, or is there a better way? (Though a full nexus parser 
and flexible outputter looks like a nightmare...)

Thanks,

Matthew

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