Tuesday, May 21, 2013

Version of getCladesofSize that also works for multifurcating trees

As promised earlier, I have figured out how to allow the function getCladesofSize (which gets all the subtrees of a phylogeny that cannot be further subdivided into two subtrees of size greater in size than a specified value) to allow for multifurcating, as well as strictly binary, trees. The updated code is here; and I have also posted a new version of phytools (phytools 0.2-64), which can be downloaded and installed from source.

Here's a quick demo of what the function does:

> require(phytools)
Loading required package: phytools
> packageVersion("phytools")
[1] ‘0.2.64’
> # a tree with lots of polytomies
> plotTree(tree,fsize=0.6)
> is.binary.tree(tree)
[1] FALSE
> trees<-getCladesofSize(tree,5)
> trees
6 phylogenetic trees
> layout(matrix(1:6,3,2))
> plotTree(trees)
Waiting to confirm page change...

Looking at all the trees - we can see that none can be further subdivided into two (or more, for trees polytomous at the root) reciprocally monophyletic groups all containing (in this case) 5 or more tips. Cool.

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