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Usage

 

NetMerger [-cl chainLength] [-bl burnInLength] [-sf sampleFrequency] [-outgroup outgroup] [-inputFolder inputFolder]



 

-cl chainLength

The length of the MCMC chain.

required

-bl burnInLengthThe number of iterations in burn-in period of MCMC inference.required

-sf sampleFrequency

The sample frequency in MCMC inference.

required

-outgroup outgroupThe taxon in species network designated to be the "outgroup".required
-inputFolder inputFolder The folder where results of MCMC_SEQ or MCMC_BiMarkers locate. Each file ends in ".out" is a single inference of a subnetwork.required

Example

#NEXUS

BEGIN PHYLONET;

NetMerger -cl 6000000 -bl 3000000 -sf 5000 -inputFolder "/Users/zhujiafan/Documents/BioinfoData/results/"
-outgroup "Z" ;
END;

 

Suppose the number of taxa is 11. And trinets are inferred for every combination of 3 taxa. There should be 120 ".out" files under the folder "/Users/zhujiafan/Documents/BioinfoData/results/".

Command References

  1. D.Wen and L. Nakhleh. Co-estimating reticulate phylogenies and gene trees on sequences from multiple independent loci. 

See Also