I'd like to try a contact prediction method (like TripletRes, CCMpred etc) using a custom set of sequences. There are about 1.5M sequences, all very similar to the canonical sequence; their distribution reflects the occurence of mutations "in the wild" (they're not clustered or anything like that). How should I make a MSA in this case?
For example in the original TripletRes paper it looks like the MSA comes from DeepMSA - this searches UniClust30 and UniRef90 using hhblits and jackhmmer. I don't see any way to use DeepMSA to make a MSA from a fully custom set of sequences, and also it's not clear how to combine a custom set with the UniClust/UniRef search results. I can make an alignment of just my data with jackhmmer, but I don't know if that's what the other tools expect. For one thing, the alignment is pretty huge compared to the typical inputs (~million vs typical DeepMSA outputs of a few hundred); for another, it is a lot less variable (most sequences differ in just 1-2 aa, vs completely different species).