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InferNetwork_ML_CV (gene_tree_ident1 [, gene_tree_ident2...]) numReticulations [-cv numFolds] [-a taxa map] [-b threshold] [-s startingNetwork] [-h {s1 [,s2...]}] [-w (w1,w2,w3,w4...,w7)] [-f maxFailurex numRuns] [-m maxNetExamined] [-xmd numRunsmoveDiameter] [-mrd maxNetExaminedreticulationDiameter] [-d maxDiameterf maxFailure] [-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 | |||
-cv numFolds | Number of folds in K-fold cross-validation. Default value is 10. | 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 (0.1,0.151,0.15,0.255,0.5). | optional | -f maxFailure | The maximum number of consecutive failures before the search terminates. Default value is 10015,0.15,2.8). | 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 | |||
-d maxDiametermd 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. | ||||
-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 | |||
-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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Y. Yu, J. Dong, K. Liu, and L. Nakhleh, Probabilistic inference of reticulate evolutionary histories, Under Review, Maximum Likelihood Inference of Reticulate Evolutionary Histories, Proceedings of the National Academy of Sciences, vol. 111, no. 46, pp. 16448-16453, 2014.