Table 2.

Comparison of alignment quality by the different methods on different sets of alignment benchmarks measured using the average SP score

	PEbA_ProtT5	PEbA_ESM2	BLOSUM62	DEDAL	vcMSA
RV11	0.590	0.336	0.220	0.413	0.559
RV12	0.844	0.715	0.626	0.648	0.828
RV911	0.461	0.242	0.276	0.092	0.437
RV912	0.755	0.633	0.594	0.377	0.685
RV913	0.940	0.900	0.874	0.203	0.922

FATCAT is not shown in this table because it was tested only on RV11 where it achieved an average SP score of 0.603