BARCE settings

Model options

This uses the F84 (Felsenstein 84) model of nucleotide substitution, estimates both the initial stationary frequencies and the transition-transversion ratio from the data, sets the initial recombination parameter lambda (the probabilistic equivalent to the recombination cost in RECPARS ) to 0.9, selects a uniform a priori distribution on the tree topologies, and reads in the initial state sequence from mosaic.in. This initial state sequence is set to a uniform sequence of the global maximum likelihood topology - this is the topology one gets when applying standard maximum likelihood, as implemented, for instance, in PHYLIP, to the whole sequence alignment without correcting for recombination.

mosaic.in
2
500
0 0


For further information on the parameters, click here.

Run settings menu

Length of the burn-in period	B	100000
Length of the sampling period	.	100000
Number of points to return	N	1000
Thinning interval	I	100
Tuning interval (for proposal distributions)	C	100
Update lambda with Gibbs sampling	W	YES
Annealing scheme for lambda	Q	PAR
Update stationary frequencies in MCMC algorithm	U	YES
Update transition-transversion ratio in MCMC algorithm	A	YES
Branch length in initial trees	O	0.1

We choose an equilibration (or burn-in) period of 100,000 MCMC steps, after which 1000 configurations are sampled in intervals of 100 MCMC steps, amounting to 100,000 MCMC steps altogether. During equilibration, the parameters of the proposal distribution are adjusted in intervals of 100 MCMC steps. We sample the transition-transversion ratio, the nucleotide stationary frequencies and the recombination parameter lambda from the posterior distribution, and apply the PAR version of simulated annealing. The initial branch length should be set to the average value of the global maximum likelihood tree, 0.1 in this case. For further information on the parameters, click here.

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