Description
Merge subnetworks inferred by MCMC_SEQ or MCMC_BiMarkers.
Usage
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-cl chainLength | The length of the MCMC chain. | required |
-bl burnInLength | The number of iterations in burn-in period of MCMC inference. | required |
-sf sampleFrequency | The sample frequency in MCMC inference. | required |
-outgroup outgroup | The 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/" |
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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
- D.Wen and L. Nakhleh. Co-estimating reticulate phylogenies and gene trees on sequences from multiple independent loci.