We first parsed and formatted the five pairs of paralogous gene families that were filtered in previous steps of the study and generated a concatenated alignment and a 5-partition alignment. See link for more details on data formatting. (2/n) github.com/sabifo4/LUCA...

Once we had our sequence alignment, we inferred and calibrated the tree topology that we fixed in the subsequent timetree inference analyses with PAML. See link for more details on these steps. (3/n) github.com/sabifo4/LUCA...