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

Nathan Haigh n.haigh at sheffield.ac.uk
Thu Nov 9 08:55:59 EST 2006

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.
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Hi Albert,

I don't know if you are aware of this resource, so here it is:

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.


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