[Bioperl-l] Query on tree bootstrap values
Nathan S. Haigh
n.haigh at sheffield.ac.uk
Fri Oct 27 12:24:49 UTC 2006
> Ah, well from a brief google it seemed like some software do store
> boostrap values for internal nodes as the node ids when outputting in
> Newick format. I don't think Bioperl should be able to tell the
> difference between a normal id and a bootstrap value, so you'll have
> to detect that yourself and manually use bootstrap() when you get an
> id that looks like a number.
If I remember rightly, in programs like Clustal you can specify where
bootstrap values are stored - node or branch. I can't remember which is
the default way, but TreeView can only see bootstraps in they are stored
using the "non-default" setting. This "could" be the same issue here.
> Or should Bioperl be making this assumption for you? Is that a safe
> thing to do? Maybe as an option only?
I don't know without a closer look - i'd also need to look at the newick
format definition as to whether this is an "extension" to the format or
if something is just flouting the newick rules.
More information about the Bioperl-l