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InferNetwork_MP (gene_tree_ident1 [, gene_tree_ident2...]) numReticulations [-a taxa map] [-b threshold] [-s startingNetwork] [-fs] [-n numNetReturned] [-m maxNetExamined] [-d maxDiameter] [-h {s1 [,s2...]}] [-w (w1,...,w6)] [-f maxFailure] [-x numRuns] [-pl numProcessors] [-di] [resultOutputFile]
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gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited list 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 1. | optional |
-m maxNetExamined | Maximum number of network topologies to examined. Default value is infinity. | optional |
-d maxDiameter | Maximum diameter to make an arrangement during network search. Default value is infinity. | optional |
| -h {s1 [, s2...]} | A set of specified hybrid species. | optional |
| -w (w1, ..., w6) | 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). | optional |
| -f maxFailure | The maximum number of consecutive failures before the search terminates. Default value is 100. | optional |
-x numRuns | The number of runs of the search. Default value is 5. | 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, R.M. Barnett, and L. Nakhleh. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology, vol. 62, no. 5, pp. 738-751, 2013.
- Y. Yu, N. Ristic and L. Nakhleh. Fast algorithms and Heuristics for Phylogenomics under hybridization and incomplete lineage sorting. BMC Bioinformatics, vol. 14, no. Suppl 15, p. S6, 2013.
- Y. Yu, J. Dong, K. Liu, and L. Nakhleh, Probabilistic inference of reticulate evolutionary histories, Under Review.
- Z. Cao, J. Zhu and L. Nakhleh. Empirical performance of tree-based inference of phylogenetic networks. WABI 2019, vol. 143, 21: 1--21:13.