Generating Multiple Alignment Format file (Maf)

Question

[roz_safavi]

Hello,

I have 3 fasta files which I'd like to perform multiple alignment on them and generate "Multiple Alignment Format" output. I was wondering if anyone knows how to do that? I was thinking about Mafft, but Mafft does not produce maf output.

Best,
Rojin

[roz_safavi]

I'm working on relatively short sequences right now ( around 200) but this is my test set. Later I'm gonna apply the pipeline to larger sequences around 1k-5k. I was thinking about that, but Last does not do multiple laingmnet (>2 sequences), correct?

[GenoMax]

Do you have a specific need for MAF format alignments?

[roz_safavi]

Yes, I need to have a maf format so that I can use maf2hal tool to convert maf to hal format

Answer 1

[sina.majidian]

It's an old post but might help someone: Mugsy is an option. Progressive cactus also generates HAL file, which could be converted to maf with cactus-hal2maf (as part of cactus).