#t_coffee — Public Fediverse posts

@foaylward
2) If you want both core + #accessory_genomes and to capture more complex variation, perhaps a first-pass sanity check is to venture into the reference-free whole-genome "subset” aligners. Two I would recommend are #ProgressiveMauve and #Mugsy. This class of algorithms typically feature some sort of seeding, anchoring, then extensions to identify locally colinear blocks (LCBs), then a more "global" multiple sequence alignment using something like #MUSCLE or #T_Coffee.