Figure 5
From: Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Procedure for simulating sequences. From a random ancestral sequence and one or more random rate matrices, we evolve a tree of 8 or 16 sequences. We then choose all combinations of three sequences (shown), or, for pairwise comparisons, two sequences (not shown), from the tree. For each sequence pair or triple, we infer by counting the directed changes in each of the two sister sequences (relative to the outgroup), and infer by taking the log of (after normalization to make the rows sum to 1). The inferred rate matrix may contain negative off-diagonal elements (shown in red); note the error in the corresponding elements of Q and (e.g. the first element highlighted in blue). Finally, we combine the Q from each triple and derive summary statistics.