Improve colabfold MSAs to include unpaired MSA hits #213
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Description
Update MSA logic for MSA server queries to include both paired and unpaired MSA rows.
Motivation
When invoking the colabfold MSA server in paired mode, the MSAs returned only include those that could be matched on species (i.e., paired). However, there are usually many more MSAs that couldn't be matched on species. This updates logic to include those as well, resulting in much deeper MSAs in typical cases.
Our preprint also uses similar logic, where we we use both paired and unpaired MSAs, so this brings the behavior when using the mmseqs MSA option closer to that.
Test plan
Tested locally on: