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Figure 6 | BMC Bioinformatics

Figure 6

From: Using the nucleotide substitution rate matrix to detect horizontal gene transfer

Figure 6

Model parameters varied during simulated evolution of phylogenies. The total number of nodes n corresponds to the number of sequences (taxa) at the end of the simulation. The sequences are evolved so that sister taxa have an average percent divergence d; the length of time from each terminal taxon to its most recent common ancestor is d/2. The rate matrix Q1 is fixed over the whole tree, except where the simulated horizontal transfer event occurs. The modeled HGT event occurs between the second and third internal branch points and is represented by evolving one of the four taxa according to a different rate matrix Q2. (Note that if no HGT event is modeled, Q2 = Q1). To vary how far back in time the simulated HGT event occurred, we varied the ratio r betweeen the first branch and all other branches. Larger r corresponds to a more recent HGT event. The parameters were: n = 8 or 16, d was between 0.05 and 0.5 in steps of 0.05, and r was 1, 2, 5, 10, or 20. The first rate matrix Q1 was chosen randomly. In the "unconstrained" case, Q2was chosen randomly, independent of Q1. In the "constrained" case, we required that each random element of Q2 be within a certain percentage of the corresponding element of Q1; percentages of 20%, 50%, and 90% were considered.

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