Fig. 2

Comparison of the performance of PEbA and other tested methods on the reference alignments with low pairwise identity (<20%). Red points indicate an alignment where PEbA had a higher SP score relative to the reference than the other method (i.e., PEbA outperformed), and vice versa for blue points (i.e., PEbA underperformed). A–B PEbA with ProtT5 embeddings (PEbA_ProtT5) compared to PEbA with ESM-2 embeddings (PEbA_ESM2) for pairwise alignments from RV11 and RV911, respectively. C–D PEbA with ProtT5 embeddings compared to BLOSUM. E–F PEbA with ProtT5 embeddings compared to DEDAL. G–H PEbA with ProtT5 embeddings compared to vcMSA