Table 1

Factors analyzed in the alignment simulations, related program parameters and values used to simulate the sequences.

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)

* only for tree A (Figure 2)

Nuin et al. BMC Bioinformatics 2006 7:471   doi:10.1186/1471-2105-7-471