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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)
  1. * only for tree A (Figure 2)