The current MAF/multiz alignment to use is based off of hg19. There are older builds, yet this is the latest for human.
Updating to hg38 is not an immediate goal, but I will add it to the request list (scroll down to see the post: https://github.com/galaxyproject/galaxy/issues/1470).
Thanks, Jen, Galaxy team
Thank you for your help and explaining in detail.
From the UCSC download link, I am trying to download the multiz100way alignments. In the "maf" folder, I can see several maf.gz files for all the chromosomes. Some of the them are like chr22.maf.gz and so on... and some of them are like chr22_GL383583v2_alt.maf.gz and chr22_KI270731v1_random.maf.gz. Please see the screenshot of files listed in the folder (attached below). There is nothing in README to explain what is in these files. Do I just need the chromosome files (chr22.maf.gz) or all the files (every file related to the chromosome)?
Your help is much appreciated.