Additional file 3.

Supplementary Table S2, Analyses of the 33 taxa and 3 mitochondrial gene data sets. Dependency of clade support on codon positions ("Cod. pos."), amino-acid translation and on assumptions of various probabilistic models of substitution (GTRnt, GTRaa and JTT: single matrix model, CAT: site heterogeneous mixture model, BP: time heterogeneous model). Rates across site model components are defined as + Γ4 + I under maximum-likelihood (ML) and as + Γ4 under Bayesian (BI) methods. Cells display support as [PP, SH, BS], with PP: posterior probability (BI), SH: Shimodaira-Hasegawa-like support (ML), and BS: bootstrap support (ML). "*": not applicable. Main lineages of mammal parasites are defined according to their host preference: "Rodent", "Primate" and "Great Ape" (see Additional file 1, Table S1).

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Blanquart and Gascuel BMC Evolutionary Biology 2011 11:70   doi:10.1186/1471-2148-11-70