• InferNetwork_ML_Bootstrap
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Description

Infers a species network from a collection of gene trees with parametric bootstrap.

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

-sr samplingRoundsNumber of sampling processes repeated in parametric bootstrap. Default value is 100.optional
-blInclude the branch lengths of the gene trees in the inference. The gene trees need to be ultrametric and branch lengths need to be in coalescent units.optional
-ms MSCommandThe path of the executable of MS software. Must be specified if -bl above is used.optional
-em softwired | hardwired

The method that is used for evaluate the support of the branches in the inferred network. Options include softwired and hardwired cluster-based method.

By default, softwired is used.

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.optional
-oIf specified, after the search the returned species networks will be optimized for their branch lengths and inheritance probabilities.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

In parametric bootstrap, the sampling process is repeated 100 times. Users can change this number using option -sr.

By default, only topologies of the gene trees are used in the computation. However, users can use option -bl to include the branch lengths of the gene trees in the computation. If so, the input gene trees must be
ultrametric and the branch lengths need to be in coalescent units. By specifying option -bl, users need to have MS software (Hudson R.R. 2002) downloaded (http://home.uchicago.edu/~rhudson1/source/mksamples.html),
and then provide the executable including its path through option -ms. For example, if having the executable locally at /tools/MS/ms, then "-ms /tools/MS/ms" needs to be specified. Note that it is not necessary if
only topologies of the gene trees are used (not using -bl). 

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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