FAMSA Added functionality to allow profile profile alignment

I sometimes have alignments whose internal structure I do not wish to change, but I would like to align the two alignments to try to minimize inter-alignment distance. I wrote up some functionality to do this. The command would be... ./famsa --ppalign profile1 profile2 merged_profile

Jul 12 '22 19:07 sachdved

Wow, thanks for adding this useful feature! Once we add tests for this functionality to the workflow, I'll merge PR into the public repo.

Jul 14 '22 11:07 agudys

Hi Adam,

How should we handle these branch conflicts?

Sep 30 '22 19:09 sachdved

Hello @sachdved!

Sorry that your PR is still not merged. This is because we've been recently having many features/fixes under development. Actually, the fact that one of them was almost ready at the time you made a PR was the reason we didn't merged it immediately. I will take care of your PR soon (I'll resolve the conflicts).

Best, Adam

Sep 30 '22 20:09 agudys

@sachdved I incorporated your pull request with some refactorings and added profile-profile aligments in the latest commit. The syntax is a bit different, though. Instead of a separate switch, you need to specify two input files: famsa <p1.fasta> <p2.fasta> <out.fasta>. One more remark: output profiles of size smaller then 1000 are by default subject to refinement (similarly as in traditional alignment). Thus, if you do not want to change their internal structure, you need to disable refinement: famsa -refine_mode off <p1.fasta> <p2.fasta> <out.fasta>. Please let me know, if everything works as expected.

Oct 05 '22 11:10 agudys

Sounds fantastic. Thank you so much for doing that! Excited to learn from the way you refactored it.

Oct 11 '22 20:10 sachdved