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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 |
-s startingNetwork | Specify the network to start search. Default value is the optimal MDC tree. | optional |
| -fs | ||
-n numNetReturned | Number of optimal networks to return. Default value is 5. | 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 10. | 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 under full likelihood. 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 |
resultOutputFile | Optional file destination for command output. | optional |
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