Description
- Co-estimation of reticulate phylogenies (ILS & hybridization) and gene trees on sequences from multiple independent loci.
Usage
Bayesian Inference
MCMC_SEQ [-cl chainLength] [-bl burnInLength] [-sf sampleFrequency] [-sd seed] [-pl parallelThreads] [-mr maxReticulation] [-pp poissonParameter] [-tp temperatureList] [-sn startingNetworkList] [-tm taxonMap] |
| MCMC Settings | ||
-cl chainLength | The length of the MCMC chain. The default value is 1,000,000. | optional |
| -bl burnInLength | The number of iterations in burn-in period. The default value is 200,000. | optional |
-sf sampleFrequency | The sample frequency. The default value is 5,000. | optional |
| -sd seed | The random seed. The default seed is 12345678. | optional |
| -pl parallelThreads | The number of threads running in parallel. The default value is the number of threads in your machine. | optional |
| -mr maxReticulation | The maximum number of reticulation nodes in the sampled phylogenetic networks. The default value is 5. | optional |
| -outDir outDirectory | The absolute path to store the output files. The default value is the home directory. | |
| Prior Settings | ||
| -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 |
| -pp poissonParameter | The Poisson parameter in the prior on the number of reticulation nodes. The default value is 1.0 | 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 |
| -stree startingGeneTreeList | Comma delimited list of gene tree identifiers or comma delimited list of sets of gene tree identifiers. See details. The default gene trees is the UPGMA tree constructed based on Jukes-Cantor distances calculated from sequences. | optional |
| -snet startingNetwork | The network identifier. The default network is the MDC tree inferred from the starting gene trees. | optional |
Command References
- D.Wen and L. Nakhleh. Co-estimating reticulate phylogenies and gene trees on sequences from multiple independent loci. Submitted.