Are branch lengths measured in substitutions/codon or substitutions/base pair?

[Михаил Щелкунов]

I have run a phylogenetic analysis by bppml. Among the produced files is a tree with branch lengths. Are these branch lengths measured in substitutions per codon (as in PAML) or in substitutions per base pair (as in, for example, RAxML)? Maybe this is written in the manual, but I haven't found this information.

Would be grateful for help

[Laurent Guéguen]

Hello,

they are in substitutions per site, where the "site" nature depends on the model. With a codon model (such a YN98), a site is a codon,

with a nucleotide model (such as K80) a site is a nucleotide.

Cheers,

Laurent