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InferNetwork_ML_Bootstrap (gene_tree_ident1 [, gene_tree_ident2...]) numReticulations [-sr samplingRound] [-bl] [-ms MSCommand] [-em softwired|hardwired] [-a taxa map] [-b threshold] [-s startingNetwork] [-h {s1 [,s2...]}] [-w (w1,w2,w3,w4...,w7)] [-x numRuns] [-m maxNetExamined] [-md moveDiameter] [-rd reticulationDiameter] [-o] [-p (rel,abs)] [-r maxRounds] [-t maxTryPerBr] [-i improveThreshold] [-l maxBL] [-pl numProcessors] [-di] [result output fileresultOutputFile] |
gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited list of gene tree identifiers. See details. | mandatory |
numReticulations | Maximum number of reticulations to added. | mandatory |
-sr samplingRounds | Number of sampling processes repeated in parametric bootstrap. Default value is 100. | optional |
-bl | Include the branch lengths of the gene trees in the inference. The gene trees need to be ultrametric and branch lengths need to be in coalescent units. | optional |
-ms MSCommand | The path of the executable of MS software. Must be specified if -bl above is used. | optional |
-em softwired | hardwired | The method that is used for evaluate the support of the branches in the inferred network. Options include softwired and hardwired cluster-based method. By default, softwired is used. | optional |
-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 |
-h {s1 [, s2...]} | A set of specified hybrid species. The size of this set equals the number of reticulation nodes in the inferred network. | optional |
-w (w1, w2, w3, w4..., 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 |
-o | If specified, after the search the returned species networks will be optimized for their branch lengths and inheritance probabilities. | 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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