• InferNetwork_ML_CV Command
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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

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 numFoldsNumber 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 reticulationDiameterMaximum diameter for a reticulation event (the distance between two parents of a reticulation node). Default value is infinity. 
-f maxFailureMaximum consecutive number of failures for hill climbing. Default value is 100.optional
-oIf 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
-diOutput 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

 

 

Command References

  • Y. Yu, J. Dong, K. Liu, and L. Nakhleh, Maximum Likelihood Inference of Reticulate Evolutionary HistoriesProceedings of the National Academy of Sciences, vol. 111, no. 46, pp. 16448-16453, 2014.



See Also

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