Hi everybody,

I am trying to set up a dating analysis in MrBayes with a large dataset. Everything should be fine so far (following the primate tutorial), I tried both setting up a prior for the tree height and constraining the root with a time calibration (in mya) along with other calibrated constraints. I would like to do a stepping stone analysis to find the best clock model in advance also, but I have no idea what to set in clockratepr. Everything I tried gives me errors like

"Calibrated trees require compatible clockrates" or "Branch lengths of the tree does not satisfy clock" when I try to go for default (=fixed at 1 :~ substitution units=time units)

Thanks for reading this so far

Michael

Parameters

---------------------

Revmat 1

Statefreq 2

Shape 3

Pinvar 4

Ratemultiplier 5

Topology 6

Brlens 7

Igrvar 8

Igrbranchrates 9

Clockrate 10

---------------------

1 -- Parameter = Revmat

Type = Rates of reversible rate matrix

Prior = Dirichlet(1.00,1.00,1.00,1.00,1.00,1.00)

2 -- Parameter = Pi

Type = Stationary state frequencies

Prior = Dirichlet

3 -- Parameter = Alpha

Type = Shape of scaled gamma distribution of site rates

Prior = Exponential(1.00)

4 -- Parameter = Pinvar

Type = Proportion of invariable sites

Prior = Uniform(0.00,1.00)

5 -- Parameter = Ratemultiplier

Type = Partition-specific rate multiplier

Prior = Dirichlet(1.00)

6 -- Parameter = Tau

Type = Topology

Prior = Prior on topologies obeys constraints

Subparam. = V

7 -- Parameter = V

Type = Branch lengths

Prior = Clock:Uniform

Node depths are constrained by the following age constraints:

-- The age of node 'constraint1' is Lognormal(472.00,0.30)

[...]

-- Tree age has a Gamma(1.00,1.00) distribution

Subparam. = IgrBrlens

8 -- Parameter = Igrvar

Type = Variance increase of igr model branch lenths

Prior = Exponential(10.00)

Subparam. = IgrBrlens

9 -- Parameter = IgrBrlens

Type = Branch lengths of IGR relaxed clock

Prior = Gamma (expectation = v, variance = Igrvar * v)

[where v is branch length]

10 -- Parameter = Clockrate

Type = Base rate of clock

Prior = Normal(1.80,1.00)

The clock rate varies according to an independent gamma (white noise) model