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CalGTProb network_ident geneTreeList [-a taxa map] [-b threshold] [-bl] [-o] [-p (rel,abs)] [-r maxRounds] [-t maxTryPerBr] [-i improveThreshold] [-l maxBL] [-x numRuns] [-pl numProcessors] [-m ac|mul] [result outputFileresultOutputFile] |
network_ident | The name of the network. See details. | mandatory |
geneTreeList | Comma delimited list of gene tree identifiers or comma delimited list of sets of gene tree identifiers. See details. | mandatory |
| -m ac or mul | Specify the algorithm used for computation (see reference). The default value is ac. | optional |
-a taxa map | Gene tree / species tree taxa association. | optional |
| -b threshold | Specifies gene trees bootstrap threshold. Edges in the gene trees that have support lower than threshold will be contracted. | optional |
| -bl | The branch lengths of the input gene trees need to be considered in the computation | optional |
| -o | The network has only topologies, so the branch lengths and inheritance probabilities of it need to be optimized. | optimal |
-p (rel, abs) | The original stopping criterion of Brent’s algorithm. Default value is (0.01, 0.001). | optional |
-r maxRound | Maximum number of rounds to optimize branch lengths for a network topology. Default value is 100. | optional |
-t maxTryPerBr | Maximum number of trial per branch in one round to optimize branch lengths for a network topology. Default value is 100. | optional |
-i improveThreshold | Minimum threshold of improvement to continue the next round of optimization of branch lengths. Default value is 0.001. | optional |
-l maxBL | Maximum branch lengths considered. Default value is 6. | optional |
-x numRuns | The number of runs of optimizing branch lengths and inheritance probabilities. Default value is 5. | optional |
-pl numProcessors | Number of processors if you want the computation to be done in parallel. Default value is 1. | optional |
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