Could the multiple alignment generated by Roary and other softwares be directly converted to XMFA format?

[Dx-wmc]

Hey there,

Before diving into mcor, I noticed we need to set up some XMFA files. I've been using AssemblyAlignmentGenerate, which you've recommended in the past. It's a solid tool, but I've been feeling it's a little rigid, especially when we have innovative tools like Bakta and Panaroo coming up.

The part that trips me up in AssemblyAlignmentGenerate is when it has to transform Roary's output into XMFA format. You know, Roary and some other tools can autonomously spit out multiple sequence alignments of core genes using the "-e" parameter. If we could jump right from these alignments to XMFA format, it would be a great enhancement.

So, here's a thought. What if you consider weaving in a feature that directly flips these multiple sequence alignments, those produced by Roary for instance, into XMFA format? I feel like this tweak could seriously streamline the workflow, adding more flexibility and ramping up the efficiency. What do you think?