Estimating divergence from EPO ancestral sequences in primates

Question

[spiral01]

Hi, I am trying to estimate mutation rates in humans, chimps and vervets, using ancestral sequences that have been estimated using the EPO pipeline (available here from Ensembl: https://ftp.ensembl.org/pub/release-100/fasta/ancestral_alleles/).

Previously I have downloaded orthologous sequences, aligned them using MUSCLE, and then compared pairwise differences. However the ancestral sequence data is by chromosome so I am not sure how to proceed? Is it best to align chromosomes? In which case how do I deal with chromosomes that only exist in one of my three species?

What i'd really like is some direction or a pipeline for taking these ancestral sequences and estimating divergence from them, which I can then use to estimate mutation rates.