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. 2012 Jan 28;28(8):1170–1171. doi: 10.1093/bioinformatics/bts058

Fig. 2.

Fig. 2.

The indel rate of the SIV/HIV gp120 protein has most of its probability mass concentrated between 0.04 and 0.06 indels per substitution. handalign was run for 90 min on a 3.4 GHz CPU, generating 2000 samples (500 discarded as burn-in). Every fifth sample is plotted; the entire trace was used to estimate the density.