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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,w2,w3,w4...,w6)] [-f maxFailure] [-x numRuns] [-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 |
-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. The size of this set equals the number of reticulation nodes in the inferred network. | optional |
| -w (w1, w2, w3, w4..., w6) | The weights of operations for network arrangement during the network search. Default value is (0.1,0.1,0.15,0.1555,0.215,0.515). | 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 105. | 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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Simple hill climbing is used for the search. Users can specify the weights of four six operations for network arrangement through option -w. The six weights correspond to adding a reticulation node, deleting a reticulation node, relocating the head of a reticulation edge, relocating the tail of an edge, reversing the direction of a reticulation edge and replacing a reticulation edge, respectively. By default, the search terminates when a preset limit of consecutive failures is reached (Default is 100, but users can change it through option -f). However, option -m allows users to specify the maximum number of networks examined during the search. Once that number is reached, the program will terminate and return the optimal network found so far. On the other hand, users can use option -d to specify the maximum diameter of an operation for network rearrangement, like what local-SPR does. In order to avoid getting stuck at some local optimum, it is recommended to performed the search multiple times, which users can specify by option -x.
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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.
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