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Bayesian Inference
MCMC_GT geneTreeList [-cl chainLength] [-bl burnInLength] [-sf sampleFrequency] [-sd seed] [-pp poissonParameter] [-mr maximumReticulation] [-pl parallelThreads] [-tp temperatureList] [-sn startingNetworkList] [-tm taxonMap] [-pseudo] |
| geneTreeList | Comma delimited list of gene tree identifiers or comma delimited list of sets of gene tree identifiers. See details. | mandatory |
-cl chainLength | The length of the MCMC chain. The default value is 1,100,000. | optional |
| -bl burnInLength | The number of iterations in burn-in period. The default value is 100,000. | optional |
-sf sampleFrequency | The sample frequency. The default value is 1,000. | optional |
| -sd seed | The random seed. The default seed is 12345678 | optional |
-pp poissonParameter | The Poisson parameter in the prior on the number of reticulation nodes. The default value is 1.0 | optional |
| -mr maximumReticulation | The maximum number of reticulation nodes in the sampled phylogenetic networks. The default value is infinity. | optional |
| -pl parallelThreads | The number of threads running in parallel. The default value is 1. | optional |
| -tp temperatureList | The list of temperatures for the Metropolis-coupled MCMC chains. For example, a list (1.0, 2.0, 3.0) indicates a cold chain with temperature 1.0 and two hot chains with temperatures 2.0 and 3.0 respectively will be run. The first value in the list should always be 1.0. The default list is (1.0). | optional |
| -sn startingNetworkList | Comma delimited list of network identifiers. See details. If the list contains only one network, the network will be used as the starting network for all the chains. If the length of the list equals to the the length of the temperature list, each chain will have a corresponding starting network. The default list is empty and the MDC tree will be used as the starting network. | optional |
| -tm taxonMap | Gene tree / species tree taxa association. By default, it is assumed that only one individual is sampled per species in gene trees. However, this option allows multiple alleles to be sampled. | optional |
| -pseudo | Use pseudo likelihood instead of full likelihood to reduce runtime, see details. | optional |
Summarization
MCMC_GT -sum fileList |
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