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InferNetwork_ML geneTreeList numReticulations [-a taxa map] [-bl] [-b threshold] [-s startingNetwork] [-n numNetReturned] [-h {s1 [,s2...]}] [-w (w1,...,w7)] [-x numRuns] [-m maxNetExamined] [-md moveDiameter] [-rd reticulationDiameter] [-f maxFailure] [-o] [-po] [-p (rel,abs)] [-r maxRounds] [-t maxTryPerBr] [-i improveThreshold] [-l maxBL] [-pl numProcessors] [-di] [result output fileresultOutputFile] |
geneTreeList | Comma delimited list of gene tree identifiers or comma delimited list of sets of gene tree identifiers. See details. | mandatory |
numReticulations | Maximum number of reticulations to added. | mandatory |
-b threshold | Gene trees bootstrap threshold. Edges in the gene trees that have support lower than threshold will be contracted. | optional |
-a taxa map | Gene tree / species tree taxa association. | optional |
-bl | Use the branch lengths of the gene trees for the inference. | optional |
-s startingNetwork | Specify the network to start search. Default value is the optimal MDC tree. | optional |
-n numNetReturned | Number of optimal networks to return. Default value is 1. | optional |
-h {s1 [, s2...]} | A set of specified hybrid species. | optional |
-w (w1, ..., w7) | The weights of operations for network arrangement during the network search. Default value is (0.1,0.1,0.15,0.55,0.15,0.15,2.8). | optional |
-x numRuns | The number of runs of the search. Default value is 5. | optional |
-m maxNetExamined | Maximum number of network topologies to examined. Default value is infinity. | optional |
-md moveDiameter | Maximum diameter to make an arrangement during network search. Default value is infinity. | optional |
-rd reticulationDiameter | Maximum diameter for a reticulation event (the distance between two parents of a reticulation node). Default value is infinity. | optional |
-f maxFailure | Maximum consecutive number of failures for hill climbing. Default value is 100. | optional |
-o | If specified, during the search, for every proposed species network, its branch lengths and inheritance probabilities will be optimized to compute its likelihood. Default value is false. | optional |
-po | If specified, after the search the returned species networks will be optimized for their branch lengths and inheritance probabilities. Default value is false. | optional |
-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 |
-pl numProcessors | Number of processors if you want the computation to be done in parallel. Default value is 1. | optional |
-di | Output the Rich Newick string of the inferred network that can be read by Dendroscope . | optional |
result output fileresultOutputFile | Optional file destination for command output. | optional |
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During the search, by default, simulated annealing is used (See Salter and Pearl 2001 for details of settings), where the branch lengths and inheritance probabilities are sampled. In this case, through option -po, as a post-processing, users can optimize the branch lengths and inheritance probabilities of the species networks returned by the search. If the dataset is not large and a large a mount of memory is available, users can use option -o to optimize the branch lengths and inheritance probabilities of every proposed network during the search. In this case, simple hill climbing will be used, and only the first 5 operations for network arrangement will be used. If branch lengths of the gene trees are used (option -bl), the latter case will be applied.
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