Figure 1.
The CPU times required for various sizes of alignments. Sequences were generated using the ROSE program (29). (A and B) Average length (L) of input sequences versus CPU time. The number of sequence is 40. Average distance among input sequences is 100 PAM (A) (percentage identity ∼ 35–85) or 250 PAM (B) (percentage identity ∼ 15–65). (C and D) The number of input sequences (N) versus CPU time. Average sequence length is 300. Average distance among input sequences is 100 PAM (C) or 250 PAM (D). See Table 1 for command-line options for each strategy in MAFFT. Options of other programs are as follows:
- TCoffee, default;
- PROBCONS, default;
- CLUSTAL W, default;
- MUSCLE-i, muscle -maxiters 16;
- MUSCLE-2, muscle -maxiters 1;
- MUSCLE-fast, muscle -sv -maxiters 1 -diags1 -distance1 kbit20_3.