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| ML Settings | |||||
| -mnr numRuns | The length of the MCMC chainnumber of iterations of simulated annealing. The default value is 100. | optional | |||
-mec maxExaminationsCount | The maximum allowed times of examining a state during one iteration. The default value is 50,000. | optional | |||
-mno numOptimums | The number of optimal networks to print. The default value is 10. | optional | |||
| -mf maxFailures | The maximum allowed times of failures to accept a new state during one iteration. The default value is 50. | optional | |||
| -pl parallelThreads | The number of threads running in parallel. The default value is the number of threads in your machine. | optional | |||
| MC3 Inference Settings | |||||
| -mc3 temperatureList | The list of temperatures for the Metropolis-coupled MCMC chains. For example, -mc3 (2.0, 3.0)indicates two hot chains with temperatures 2.0 and 3.0 respectively will be run along with the cold chain with temperature 1.0. By default only the cold chain will be run. Note that
| optional | |||
| Inference Settings | |||||
| pseudo | Use pseudolikelihood. | optional | |||
| -mr maxReticulation | The maximum number of reticulation nodes in the sampled phylogenetic networks. The default value is 4. | optional | |||
| -taxa taxaList | The taxa used for inference. For example, -taxa (a,b,c) | required | |||
| -tm taxonMap | Gene tree / species tree taxa association. By default, it is assumed that only one individual is sampled per species in gene trees. This option allows multiple alleles to be sampled. For example, the gene tree is (((a1,a2),(b1,b2)),c); and the species tree is ((a,b),c);, the command is -tm <a:a1,a2; b:b1,b2;c:c>. Note that the taxa association should cover all species, e.g. -tm <a:a1,a2; b:b1,b2> is incorrect because c:c is dropped out. | optional | |||
| -fixtheta theta | Fix the population mutation rates associated with all branches of the phylogenetic network to this given value (theta). By default, we estimate a constant population size across all branches. | optional | -varytheta | The population mutation rates across all branches may be different when estimating them. By default, we estimate a constant population size across all branches. | optional |
| -esptheta | Estimate the mean value of prior of population mutation rates. | optional | |||
| Prior Settings | |||||
| -pp poissonParam | The Poisson parameter in the prior on the number of reticulation nodes. The default value is 1.0. | optional | |||
| -dd | Disable the prior on the diameters of hybridizations. By default this prior on is exp(10). | optional | |||
| -ee | Enable the Exponential(10) prior on the divergence times of nodes in the phylogenetic network. By default we use Uniform prior. | optional | |||
| Starting State Settings | |||||
| -snet | Specify the starting network. The input network should be ultrametric with divergence times in units of expected number of mutations per site, inheritance probabilities and population sizes in units of population mutation rate (optional). See example below. The default starting network is the MDC trees given starting gene trees. | optional | |||
| -ptheta startingThetaPrior | Specify the mean value of prior of population mutation rate (startingThetaPrior). The default value is 0.036. If -esptheta is used, startingThetaPrior will be treated as the starting value, otherwise startingThetaPrior will be treated as the fixed mean value of prior of population mutation rates. | optional | |||
Data related settings | |||||
| -diploid | Specify whether sequence sampled from diploids. | optional | |||
| -dominant dominantMarker | Specify which marker is dominant if the data is dominant. Either be '0' or '1'. | optional | |||
| -op | Specify whether or not to ignore all monomorphic sites. If this option is used, the data will be treated as containing only polymorphic sites. | optional | |||
Example
Download: run_0.nex
#NEXUS
A_0 1001011010101011001000010101010111001010011001100101111011000011111000001010001001100000110100001011 |
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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. maximum pseudolikelihood estimation of 10 iterations with 20 optimal networks printed. And after 100 times of failure to accept a new state, or after 50000 examinations of new states, it will start a new iteration. We will estimate population mutation rates for every all branches, and they may be different. A Poisson prior of 2.0 will be adopted, and a Exponential(2.0) prior will be adopted. are the same across all branches. The number of reticulation nodes is limited to 1. We will sample the mean The starting value of prior of population mutation rates, and the starting value of 0.3 is givenpopulation mutation rate is given by 0.006. We use the random seed of 12345678. In the end, we indicate the mapping from taxa to species.