.axt formats for pairwise alignments and how to convert to paml

Question

[spiral01]

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.

[AK]

You can try this one - https://github.com/bxlab/bx-python/blob/master/scripts/axt_to_fasta.py:

$ cat test.axt
0 chr19 3001012 3001075 chr11 70568380 70568443 - 3500
TCAGCTCATAAATCACCTCCTGCCACAAGCCTGGCCTGGTCCCAGGAGAGTGTCCAGGCTCAGA
TCTGTTCATAAACCACCTGCCATGACAAGCCTGGCCTGTTCCCAAGACAATGTCCAGGCTCAGA

1 chr19 3008279 3008357 chr11 70573976 70574054 - 3900
CACAATCTTCACATTGAGATCCTGAGTTGCTGATCAGAATGGAAGGCTGAGCTAAGATGAGCGACGAGGCAATGTCACA
CACAGTCTTCGCATTGAGGTACCAAGTTGTGGATCAGAATGGAAAGCTAGGCTATGATGAGGGACAGTGCGCTGTCACA

$ python axt_to_fasta.py < test.axt
>chr19_3001011_3001075
TCAGCTCATAAATCACCTCCTGCCACAAGCCTGGCCTGGTCCCAGGAGAGTGTCCAGGCTCAGA
>chr11_70568379_70568443
TCTGTTCATAAACCACCTGCCATGACAAGCCTGGCCTGTTCCCAAGACAATGTCCAGGCTCAGA

>chr19_3008278_3008357
CACAATCTTCACATTGAGATCCTGAGTTGCTGATCAGAATGGAAGGCTGAGCTAAGATGAGCGACGAGGCAATGTCACA
>chr11_70573975_70574054
CACAGTCTTCGCATTGAGGTACCAAGTTGTGGATCAGAATGGAAAGCTAGGCTATGATGAGGGACAGTGCGCTGTCACA