How to convert newick tree to ultrametric tree?

Question

[nimishabalan131]

Hi, I need to convert my newick tree to ultrametric tree for using in CAFE package. How can I convert using APE v5.4 or using any other method??

[Jean-Karim Heriche]

If your tree is supposed to already be ultrametric but fails an ultrametric test due to loss of numerical precision, then check the force.ultrametric() function in the phytools package. If your tree is not ultrametric to start with then you should look at calibrating the branch lengths with one of the chrono* functions in ape.