Read Figure7.8_part2 text version

Models supported by MrBayes 3 (simplified) Data Type Protein A-Y Model Type Equalin/GTR prset aamodelpr Poisson/Jones/ Dayhoff/Mtrev/ Mtmam/Wag/ Rtrev/Cprev/Vt/ Blossum/mixed prset aamodelpr State Frequencies fixed/est. (Dirichlet) prset statefreqpr Substitution Rates fixed/est. (Dirichlet) prset aarevmatpr Across-Site Rate Variation equal/gamma/ propinv/invgamma/ adgamma lset rates equal/gamma/ propinv/invgamma/ adgamma lset rates

page 2 Across-Tree Rate Variation yes/no lset covarion

fixed/mixed

fixed/mixed

yes/no lset covarion

Parameter Variation Across Partitions Topology Models unconstrained/ constraints/fixed constraint prset topologypr Brlens Type Fixed prset brlenspr Unconstrained prset brlenspr Clock prset brlenspr shared/separate set partition, link, unlink Inferring Site Parameters ancstates/possel/siteomega/siterate report Additional Parameters see prset (lset for diploidy) Treeheight Theta, Diploidy Growth Speciation Extinction Treeheight Sampleprob

Brlens Prior Exponential/Uniform prset brlenspr Uniform prset brlenspr Coalescence prset brlenspr Birth-Death prset brlenspr

Clockrate Variation strict/cpp/ bm/ibr prset clockratepr Dating Constraints unconstrained/ calibrated calibrate prset nodeagepr prset treeagepr

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Figure7.8_part2