I want multiple sequence alignments of few vertebrate species (Human, cow, buffalo, sheep and goats). UCSC browser has MSA for 46 vertebrate species and MSA of 3 or 4 species under individual species. But I don't find the combination I need.
Is it possible to extrat MSA of desired species from 46 vertebrate MSA? Or Is it possible to use the pairwise alignments among different species to produce MSA?
Also UCSC does not have information for buffalo. After producing the MSA for other species is it possible to add buffalo genome to the MSA?
I want to project the multiple sequence alignment to buffalo genome as reference sequence.