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
I would read the following: Yang, Z and Rannala.B. 2012. Molecular Phylogenetics: Principles and Practice. Nature Reviews Genetics. 13:303-314.
and the attached.
I am trying to figure out similar matters and find Yang to be very good on priors.
Thanks a lot, I will read them on the weekend.
It turns out that I am having additional problems like 0 branch length and incomplete data. I will have to fix that before coming back to this problem.
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