CODEWITHSUNDEEP
rstatisticsnormalizationphylogenyape-phylo
Krisrs1128
Krisrs1128

Reputation: 323

Normalizing a Phylogenetic Tree in R

When working with phylogenetic tree data in R (specifically when working with "phylo" or "phylo4" objects) it would be useful to normalize branch lengths so that certain taxa (the ones that evolve faster) do not contribute a disproportionate amount of branch length to the tree. This seems to be common in computing UniFrac values, as can be found in the discussion here: http://bmf2.colorado.edu/unifrac/help.psp. (I need more than just UniFrac values, however).

However, I cannot find a function that performs this normalization step. I have looked in ape, picante, adephylo, and phylobase. Could someone direct me to a package that includes this function, or a package that makes writing this kind of function straightforward?

Upvotes: 4

Views: 1420

Answers (1)

kmm
kmm

Reputation: 6310

Are you looking for a function to just scale the branch lengths of a tree? If so, compute.brlen() in ape will do it. There are built in options for Grafen's rho and all = 1. You can also supply your own function.

I don't know if UniFrac does some other kind of branch length scaling. But if so, you could write your function and pass it.

Upvotes: 2

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