Comparing branch lengths of phylogenies

Question

[natasha]

I have generated 2 phylogenies for same sequence data, however for one of these phylogenies I have removed recombination. The topology of the trees are therefore the same but the branch lengths are now different. Is there a way to quantify this - as in, is there an algorithm I can use to show a statistical difference between the two trees?

Answer 1

[dago]

I think that the APE package in R can compare trees. https://cran.r-project.org/web/packages/ape/ape.pdf