I am currently trying to calculate rates of substitution in humans, using the human-chimpanzee pairwise alignment found here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsPanTro6/
My problem is that the alignment is in the .axt format (explained here: https://genome.ucsc.edu/goldenPath/help/axt.html), and I need to use PAML's baseml to conduct analysis on substitution rates. PAML requires the .nuc format and I have no idea how to convert .axt to any other format. Are there any tools out there to convert to .fasta for example? Extensive searching has lead only to a discontinued tool on Galaxy. Any other suggestions would be appreciated.