[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



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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>   

-- 
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 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/
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++




More information about the Bioperl-l mailing list