Description
Infers a species network(s) using maximum likelihood, where K-fold cross-validation is used to account for model complexity. Only topologies of gene trees are used in the inference and all gene trees need to be binary.
Usage
InferNetwork_ML_CV (gene_tree_ident1 [, gene_tree_ident2...]) numReticulations [-cv numFolds] [-a taxa map] [-b threshold] [-s startingNetwork] [-h {s1 [,s2...]}] [-w (w1,...,w7)] [-x numRuns] [-m maxNetExamined] [-md moveDiameter] [-rd reticulationDiameter] [-f maxFailure] [-o] [-p (rel,abs)] [-r maxRounds] [-t maxTryPerBr] [-i improveThreshold] [-l maxBL] [-pl numProcessors] [-di] [resultOutputFile]
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. | 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 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. | |
| -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 |
resultOutputFile | Optional file destination for command output. | optional |
By default, 10-fold cross-validation is used to account for model complexity. But users can change the number of folds using option -cv.
See command InferNetwork_ML for all other parameters.
Examples
#NEXUS BEGIN TREES; TREE gt0 = (D:7.07072,((C:3.56753,B:3.56753):1.76822,A:5.33575):1.73497); TREE gt1 = (((B:1.97661,C:1.97661):2.23864,A:4.21524):1.77987,D:5.99511); TREE gt2 = ((C:4.31675,(B:3.14621,A:3.14621):1.17054):2.09695,D:6.4137); TREE gt3 = ((D:5.83927,A:5.83927):0.566624,(B:1.80987,C:1.80987):4.59603); TREE gt4 = ((D:5.77537,(B:1.77451,C:1.77451):4.00086):0.810136,A:6.58551); TREE gt5 = (D:6.80413,(A:3.82444,(C:2.31671,B:2.31671):1.50773):2.97969); TREE gt6 = (D:7.61541,(C:4.41986,(A:2.52336,B:2.52336):1.8965):3.19554); TREE gt7 = ((A:4.99068,(C:3.03372,B:3.03372):1.95696):0.782212,D:5.77289); TREE gt8 = (D:5.95232,((C:1.86462,B:1.86462):3.20304,A:5.06765):0.88467); TREE gt9 = ((A:3.84332,(C:3.74007,B:3.74007):0.103251):4.82743,D:8.67075); TREE gt10 = ((A:4.19291,(C:1.73235,B:1.73235):2.46056):2.60752,D:6.80043); TREE gt11 = (A:7.35563,((B:1.7592,C:1.7592):4.0683,D:5.8275):1.52813); TREE gt12 = (((B:3.14432,A:3.14432):0.613233,C:3.75755):1.95882,D:5.71638); TREE gt13 = (((C:2.6677,B:2.6677):2.66994,A:5.33764):4.71766,D:10.0553); TREE gt14 = ((C:4.00286,(B:3.0957,A:3.0957):0.907165):1.94607,D:5.94893); TREE gt15 = (D:5.89168,(A:3.77037,(B:2.13754,C:2.13754):1.63283):2.12131); TREE gt16 = (D:6.43412,(A:3.85214,(B:2.6542,C:2.6542):1.19794):2.58198); TREE gt17 = (D:6.27103,((B:1.80021,C:1.80021):1.91286,A:3.71307):2.55796); TREE gt18 = (((C:1.72131,B:1.72131):4.04022,A:5.76154):2.49476,D:8.25629); TREE gt19 = (((B:1.8262,C:1.8262):2.49809,A:4.32429):3.80882,D:8.13311); TREE gt20 = (D:6.95436,((B:2.60072,C:2.60072):1.85771,A:4.45842):2.49594); END; BEGIN PHYLONET; InferNetwork_ML_CV (gt0,gt1,gt2,gt3,gt4,gt5,gt6,gt7,gt8,gt9,gt10,gt11,gt12,gt13,gt14,gt15,gt16,gt17,gt18,gt19,gt20) 3 -x 5; END;
Command References
Y. Yu, J. Dong, K. Liu, and L. Nakhleh, Maximum Likelihood Inference of Reticulate Evolutionary Histories, Proceedings of the National Academy of Sciences, vol. 111, no. 46, pp. 16448-16453, 2014.