[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.


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