Fig. 7. Phylum topologies estimated from replicates abc.2 and bca.2.

HMM parameters are held fixed for making the MSAs (both have random seed 2) while the guide tree topology is permuted. All six tree estimation methods agree with each other on the topology on a given MSA, but the topologies are different so one or both topologies must be wrong and the reproducible wrong tree must be induced by guide tree bias as the MSA is otherwise unchanged. Most methods give high bootstraps (shown in table below the trees) for most or all of the edges.