Re: module Bio::TreeIO

Hi,

I can see why you were confused by the boot.phylo docs, it's not very 
clear, but it is resampling columns from an alignment.

I've uploaded a script to GitHub which does a BioPerl-based bootstrap 
analysis, maybe it will be useful for you.
https://github.com/RoyChaudhuri/bioperl-scripts/blob/master/boottree
However, I would note that BioPerl is certainly not the most efficient 
way of doing this, and neighbor-joining is not the most robust method of 
constructing a tree (more sophisticated approaches are available in 
programs such as RAxML and MrBayes).

You're right about the assess_bootstrap docs. You could post this as an 
issue on GitHub (or even better, fix it and submit a pull request):
https://github.com/bioperl/bioperl-live/issues

Cheers,
Roy.

On 10/05/2016 13:54, lskatz wrote:
> That's what I thought originally too but the R package made it look like
> there might be some magic bootstrapping going on with distances alone.  If
> there truly is no distance-matrix bootstrapping algorithm then I am left to
> my devices and at least I can make use of assess_bootstrap().
>
> By the way, if I can make a documentation bug report -- it looks like
> assess_bootstrap() only takes a list of trees as an argument but when I look
> at the source code it looks like it also can take a guide tree as a second
> parameter.  That second parameter is not in the documentation.  How would I
> specifically report that?
>
>
>
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