Enabling paired MSA generation#28
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In addition to paired MSAs, this introduces a few new arguments for controlling MSA generation. In particular:
msa_mode: This can be "paired+unpaired" (default), "unpaired", or "paired". If "paired+unpaired", both unpaired and unpaired MSAs will be generated and the unpaired MSA will be concatenated to the paired MSA. In the other two options, the only corresponding MSA is generated and used.pairing_strategy: This can be "greedy" (default) or "complete". This controls how sequences are paired when creating the paired MSA.