Description
Convert the log file generated by MCMC_SEQ to be readable by Tracer.
Usage
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| Settings | ||
-cl chainLength | The length of the MCMC chain. Set to the same value used in MCMC_SEQ. | required |
| -bl burnInLength | The number of iterations in burn-in period. Set to the same value used in MCMC_SEQ. | required |
-sf sampleFrequency | The sample frequency. Set to the same value used in MCMC_SEQ. | required |
| -outfile filename | The name of tracer log file you want to generate. Can contain path. | required |
| -truenet networkString | The network you want to summarize its parameters. | required |
Example
#NEXUS
;End; BEGIN PHYLONET; -taxa (a,b,c1,c2,d) END; |
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Note that an empty line should be left after "Matrix".
This command will run MCMC chain of 500000 iterations with 200000 burn-in iterations, and one sample will be collected every 500 iterations. The taxa are diploids and 1 is the dominant marker. Only polymorphic sites will be used. We will estimate population mutation rates for every branches, and they may be different. A Poisson prior of 2.0 will be adopted, and a Exponential(2.0) prior will be adopted. The number of reticulation nodes is limited to 1. We will sample the mean value of prior of population mutation rates, and the starting value of 0.3 is given. We use the random seed of 12345678. In the end, we indicate the mapping from taxa to species.