I have several files from a colleague that were output by Satsuma. Each file contains a different genome (query) aligned to the same reference.

The format of satsuma output files follows the form defined here. The file contains these human readable alignments. But also a file can be output which contains data in a tabula format, for example here.

Is it possible to get a multiple alignment from this output, or otherwise convert it to a form that could be used in a multiple sequence alignment? The alternative is doing a MSA from scratch.

Thanks,
Ben.