Painless (or low-pain) way of getting MAF alignment for phyloCSF (mm10)?

Question

[dvanic]

Hi All

I was wondering - what is the most pain-free (or minimal pain) way of extracting a multiple sequence alignment to use with phyloCSF? (and, thanks, yes, I know there are other tools out there which are easier to use).

I am playing with new mm10 mouse transcripts (and, yes, I've looked at Galaxy, and it only seems to have an hg19 100 species multiple sequence alignment), and if you upload the mouse 60-way alignment from UCSC (directly or via download/upload), you cannot filter by species (apparently because it's too much data , which is what I'd be keen to do.

So - how do I get a nice MAF?

Thanks in advance!

I have seen this - which deals only with hg19 human, and this and this

which seems to be most useful, except that the statement of "It is not perfectly in multi Fasta format, but it is close enough for a simple transformation." is already discouraging, not to mention that I can't see a filter MAF by species option there .

There is also this question - which unfortunately was never answered, so I'm definitely not the only one with this problem...

Also this may be useful, but I'm not sure...

Thanks in advance!

[istloui1]

https://www.gencodegenes.org/mouse/