[Bioperl-l] nexus add_tree, get_trees, write tree in write_aln

[Nathan Haigh]

Albert Vilella wrote:
> Hi,
>
> I am musing on how to add trees to the AlignIO::Nexus objects.
>
> In PAML we have this "add_tree" method, and "get_rst_trees", which we
> could also apply to this case.
>
> I also would like to hear some feedback on how to write_aln nexus
> files that contain one or more trees in the object instance. Do we
> want this by default? Only if a "with_trees" parameter is set?
>
> Cheers,
>
>     Albert.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   
Hi Albert,

I don't know if you are aware of this resource, so here it is:
http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all

I would suggest that if there are trees in the object instance, then
write_aln should print them by default and then have a "no_trees" option.

Nath