[Bioperl-l] [Summary] Re: suggestions for suitable 'taxon' object

Rutger Vos rvosa at sfu.ca
Sat Dec 23 17:17:37 EST 2006

The replies I've received so far indicate I should look into Bio::Taxon. 
I will probably come back with further questions/discussions as to how 
to link and cross reference taxa, sequences and  nodes, but for now I 
should first look at the Bio::Taxon api (and unpack my other Christmas 
gifts). Thank you for all comments and suggestions.

Happy holidays!


Rutger Vos wrote:
> Hi all,
> I am looking for a bioperl object that can be abused to function as a
> suitable 'taxon' object, where I mean 'taxon' as understood by the NEXUS
> file format (i.e. not strictly an entity from a taxonomy, but more loosely
> an OTU). 
> The object would primarily function as a way to relate nodes in trees to
> sequences in an alignment (a foreign key that both nodes and sequences refer
> to), and secondarily as the keeper of the canonical name of the OTU, such
> that a sequence named 'Homo_sapiens|EF177447.1/12-56' and a node named 'Homo
> sapiens (constrained monophyly)' can still be understood to refer to the
> same thing - the OTU 'Homo sapiens sapiens' (for example).
> I was thinking that a (possibly expanded) Bio::Species might work if there
> was some sensible way of appending references to node and sequence objects
> to it (or otherwise associate them with each other), but I am writing *to
> solicit any and all suggestions*. I am looking for something similar to
> Bio::Phylo::Taxa::Taxon.
> Any and all comments and suggestions greatly appreciated!
> Best wishes,
> Rutger Vos
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 Rutger A. Vos
 Postdoctoral research fellow
 University of British Columbia
 Personal site: http://www.sfu.ca/~rvosa
        CIPRES: http://www.phylo.org
    Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/

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