So I would like to use build a vertebrate phylogenetic tree using only species which have high-quality high-coverage sequences. However, looking at the UCSC web browser and downloads it looks like I can only download pre-computed chains and nets (I really need maf and axt files) for specific species pairs. In order to have made the whole vertebrate tree, these must exist somewhere.
If I want to have platypus and guinea pig in my genome, for example its going to take me long time to align them. Is there somewhere I can download these pre-computed axt and maf files containing the alignments for all of the species I am interested in?
Many thanks in advance,