How to extract ancestral sequence for Cow from 46 eutherian mammals EPO Ensembl?
I am trying to figure out how to extract the ancestral sequence of the bovine species from an Ensembl multiple alignment file: 46 eutherian mammals EPO. In the .emf files, I can see that there is indeed an inferred ancestral sequence for each node of the phylogenetic tree (with a different name for each block if I understand), as well as in the corresponding .maf files. I tried to use the WGAbed pacakge (henryjuho.github.io/WGAbed/) to transform the .maf files into .bed files with the cow as the reference species but I only get one matching ancestral sequence for each position in the bed file, and no information about which node it matches. Does anyone know how to extract the ancestral sequences already inferred in these .emf files please?
Thanks in advance for your help. Claire
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