Description
Computes the probabilities of gene tree topologies within log likelihood of a phylogenetic network given a collection of gene trees. The network must be specified in the Rich Newick Format.
The probabilities likelihood can be computed using only topologies of gene trees, or using both topologies and branch lengths of gene trees. The latter one requires the input gene trees to be ultrametric.
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| Code Block | ||
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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 output fileresultOutputFile] |
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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