Table 2 Several point values for the affine gap cost continuous-time functions open(t) and extend(t) for time instances associated to well known substitution matrices. The analytic functions are given in Eq. 2 and depicted in Fig. 6. The parameter values are: \(\mu _{A}=1.0023,\lambda =0.4296,r_{X}=0.6276,r_{M}=0.7500,\beta ^{\textsc {lr}}_{\infty } =0.3000,\beta ^{\textsc {lr}}_{\star } =0.2134\). The divergence parameter t has been normalized to BLOSUM62
From: Parameterizing sequence alignment with an explicit evolutionary model
% Substitutions | Divergence | Open | Extend | |
|---|---|---|---|---|
per site | time t | |||
PAM10/VT10 | 10.0 | 0.074 | –15.79 | –1.29 |
VT20 | 17.9 | 0.141 | –14.21 | –1.25 |
PAM30 | 27.1 | 0.229 | –13.14 | –1.21 |
VT40 | 32.0 | 0.283 | –12.73 | –1.18 |
PAM70 | 49.8 | 0.520 | –11.72 | –1.10 |
VT80 | 52.2 | 0.567 | –11.60 | –1.09 |
BLOSUM90 | 55.8 | 0.633 | –11.46 | –1.07 |
VT100 | 59.4 | 0.709 | –11.33 | –1.05 |
BLOSUM80 | 60.9 | 0.741 | –11.28 | –1.05 |
VT120 | 65.2 | 0.851 | –11.14 | –1.02 |
VT140 | 70.0 | 0.995 | –11.00 | –1.00 |
BLOSUM62 | 70.1 | 1.000 | –11.00 | –1.00 |
BLOSUM50 | 72.9 | 1.099 | –10.93 | –0.99 |
VT160 | 73.8 | 1.135 | –10.90 | –0.98 |
PAM120 | 74.9 | 1.180 | –10.88 | –0.98 |
BLOSUM45 | 76.3 | 1.245 | –10.84 | –0.97 |