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InferNetwork_MPL geneTreeList numReticulations [-a taxa map] [-b threshold] [-s startingNetwork] [-fs] [-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] [resultOutputFile]
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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 | Fix the start tree for search. If specified and give a start tree (-s), the search will fix the topology of the start tree. | optional | |
-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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- Y. Yu and L. Nakhleh. A maximum pseudo-likelihood approach for phylogenetic networks. Under review.
- Z. Cao, J. Zhu and L. Nakhleh. Empirical performance of tree-based inference of phylogenetic networks.