Fig. 1.

Results on 1000-sequence datasets, comparing default PASTA and PASTA+BAliPhy. Each point represents one replicate. PASTA denotes the alignment from PASTA under default settings (referred to as “PASTA(default)” in the text), and PASTA+BAli-Phy denotes the alignment after an additional iteration using BAli-Phy. Delta-RF refers to the difference between the RF error rates of ML trees computed on the estimated and true alignments. In each subfigure, a position above the 45-degree line indicates that PASTA+BAli-Phy is preferable; the axes for the subfigure for Delta-RF have been flipped to maintain this interpretation, since Delta-RF is an error metric rather than an accuracy metric