Fig. 5

SPFN of EMMA, WITCH-ng-add, and MAFFT-linsi--add when adding sequences into small random backbone alignments. The top panel denotes biological datasets, and the bottom panel denotes simulated datasets. Error bars indicate standard errors. MAFFT-linsi--add failed to finish within 24 h for datasets except for 10AA and ROSE 1000M1–4, and we did not run it on Rec or Res due to their large numbers of sequences (failed runs, or runs that were not attempted, are marked with “X”). Comparisons with MAFFT--add can be found in Additional file 1: Fig. S8. SPFN results for each of the 10AA datasets are in Additional file 1: Fig. S13