Additional file 3.

Phylogeny with Eukaryotic Dataset after recoding amino acids into six groups. The amino acids of the Eukaryotic Dataset were recoded into six groups as follows: (1) ASTGP, (2) DNEQ, (3) RKH, (4) MVIL, (5) FYW and, (6) C. This allowed the use of a 6 × 6 general time-reversible rate matrix with free parameters rather than a fixed empirical matrix. Sequence composition and among-site rate variation parameters were also free in the BI analysis, as implemented in P4 (Foster PG: Modeling compositional heterogeneity. Syst Biol 2004, 53(3):485-495); 50 000 generations, first 10 000 removed as burn-in). Numbers at branches represent PP values.

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Liu et al. BMC Evolutionary Biology 2009 9:272   doi:10.1186/1471-2148-9-272