[Bioperl-l] module Bio::TreeIO

[Ke Jiang]

If I still remember my phylogenetics correctly, the bootstrapping process
happens earlier, before a tree could be made. Bootstrapping is actually
randomly resampling the characters used for tree construction. While TreeIO
is only a tool to manipulate trees. You'll not only have to find some way
to do resampling but also tree construction, which requires specialized
applications.

Best.

Ke

On Mon, May 9, 2016 at 2:47 PM, lskatz <lskatz at gmail.com> wrote:

> I'm rehashing this old topic because it seems like the most relevant to my
> question.
>
> After making a tree from a distance matrix, how would I calculate bootstrap
> values?  I have been shown that it can be done in R, but I would want a
> pure-perl method because the rest of my code revolves around BioPerl.
> http://www.inside-r.org/packages/cran/ape/docs/boot.phylo
>
> I think that I can use Bio::Tree::Statistics to make 100 trees and then
> combine them with
>
> e.g.,
>
>
>
> However, I would be making my own version of random or jack knifed trees
> and
> it wouldn't be as well validated as something centralized.  Before I go
> down
> this road... is there any kind of standardized method in BioPerl for making
> bootstrap values from a distance matrix?
>
> Or if not, does anyone have a suggestion on how to make the 100 trees from
> the matrix?
>
>
>
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