Improving the performance of Bayesian phylogenetic inference under relaxed clock models

Table 7 Operator weights in MCMC chains

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

Note
1: Random walk operator and Swap operator in Cons configuration, Random walk operator, Scale operator and Swap operator in Category configuration.
2: The operator introduced in Appendix section 4 is used in Cons configuration, a Scale operator is used in Category configuration.
-: The parameter is not sampled and no operator is assigned.

ISSN: 2730-7182