add the possibility to use 'align' even when the clustering is not performed through PPanGGOLiN

[axbazin]

Mentionned in #56 (34th comment)

Being able to use 'align' when using an external clustering would be quite useful.

Possibilities of realizing that are either by choosing a representative sequence for each cluster somehow, or use all genes instead of a representative for the aligning part. Doing the latter should not take too long as this is not traditionally used with a lot of protein sequences as input.

[IsabelFE]

Yeah, I can see how that might take more work. Thanks for considering this for future updates.

Regards.