Figure 2.

Comparison of alignment methods. Assessment of various alignment methods under default parameters using (a) the species-tree discordance and (b) the minimum duplication tests, on eukaryotic data. Consistency-based alignment methods do not improve over scoring matrix-based methods. The relative performance between alignment programs is more variable for nucleotide data than for amino-acid data. On amino-acid data, Mafft-FFT-NS-2, DiAlign TX and Prank were never outperformed; on nucleotide data, Mafft L-INS-i (right column) was never outperformed (see also Additional file 1, Figure S6). Average compute times (per alignment) are plotted as triangles (amino-acids) and circles (nucleotides). Error bars correspond to ± 1 s.d. Significant difference from best alignment program is denoted with a minus symbol at the basis of relevant bars (Wilcoxon double-sided test, P < 0.01).