Table 1 Factors analyzed in the alignment simulations, related program parameters and values used to simulate the sequences.
From: The accuracy of several multiple sequence alignment programs for proteins
Factor | Simprot parameter | Values | Description |
|---|---|---|---|
sequence length | -r | 50, 100, 150, 200, 250, 300 | length (in amino acids) of the root sequence |
indel frequency | -g | 0.03, 0.05, 0.1, 0.15, 0.2, 0.3 | expected indel frequency (number of indels/aa) for 100PAM |
gamma alpha | -x | 0.1, 0.7, 1, 5, 10 | shape parameter of the gamma distribution of evolutionary rates |
evolutionary scale factor | -c | 2, 3, 4 | controls the expected length of indels according to the generalized Qian-Goldstein distribution |
branch length scale multiplier* | -b | 2, 3, 4 | scale lengths of all branches in the input tree equally |
terminal gaps insertion | not available | 1, 2, 3, 4, 5 | controls the frequency and lengths of terminal gaps (as a function of internal gap parameters) |