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Table 7 Operator weights in MCMC chains

From: Improving the performance of Bayesian phylogenetic inference under relaxed clock models

Operator class Name Simulated data Anolis RSV2 HIV-1 Primates
   Cons Category Cons Category Cons Category Cons Category Cons Category
rates times ConstantDistance Operator 0.2170 - 0.2248 - 0.2228 - 0.2228 - 0.2402 -
  Rate Normal Operators1 0.1302 0.2604 0.1349 0.2698 0.1337 0.2674 0.1337 0.2674 0.1441 0.2882
  UcldStdev Scale Operator2 0.0260 0.0260 0.0270 0.0270 0.0267 0.0267 0.0267 0.0267 0.0288 0.0288
  UcldMean Scale Operator - - - - 0.0089 0.0089 0.0089 0.0089 - -
  UcldMean Tree UpperDown Operator - - - - 0.0267 0.0267 0.0267 0.0267 - -
  InternalNodeTime Scale Operator 0.0174 0.0260 0.0180 0.0270 0.0178 0.0267 0.0178 0.0267 0.0192 0.0288
  RootAge Scale Operator 0.0174 0.0260 0.0180 0.0270 0.0178 0.0267 0.0178 0.0267 0.0192 0.0288
  AllNodeTimes Uniform Operator 0.1910 0.2604 0.1978 0.2698 0.1961 0.2674 0.1961 0.2674 0.2113 0.2882
Tree SubtreeSlide Operator 0.1302 0.1302 0.0989 0.0989 0.1337 0.1337 0.1337 0.1337 0.441 0.1441
  NarrowExchange Operator 0.1302 0.1302 0.0989 0.0989 0.1337 0.1337 0.1337 0.1337 0.0480 0.0480
  WideExchange Operator 0.0434 0.0434 0.0270 0.0270 0.0267 0.0267 0.0267 0.0267 0.0480 0.0480
  WilsonBalding Operator 0.0434 0.0434 0.0270 0.0270 0.0267 0.0267 0.0267 0.0267 0.0480 0.0480
  BirthRate Scale Operator 0.0434 0.0434 0.0629 0.0629 - - - - 0.0288 0.0288
  DeathRate Scale Operator - - 0.0629 0.0629 - - - - - -
  PopulationSize Scale Operator - - - - 0.0267 0.0267 0.0267 0.0267 - -
Substitution model Kappa Scale Operator 0.0087 0.0087 0.0009 0.0009 0.0009 0.0009 0.0009 0.0009 0.0192 0.0192
  Frequencies DeltaExchange Operator 0.0017 0.0017 0.0009 0.0009 0.0009 0.0009 0.0009 0.0009 0.0010 0.0010
  1. Note
  2. 1: Random walk operator and Swap operator in Cons configuration, Random walk operator, Scale operator and Swap operator in Category configuration.
  3. 2: The operator introduced in Appendix section 4 is used in Cons configuration, a Scale operator is used in Category configuration.
  4. -: The parameter is not sampled and no operator is assigned.
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BMC Ecology and Evolution

ISSN: 2730-7182

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