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Description

Uses a hidden markov to assign a species tree to each loci in data coming from a species network.

Usage

Before using this command, you need to get lib.zip. Assuming it is then unzipped to LocalPath where the unzipped folder is located,

  • Mac: use -Djava.library.path=LocalPath/lib, when launching PhyloNet from command line.
  • Linux: add LocalPath/lib to your LD_LIBRARY_PATH, before launching PhyloNet from command line.
  • Windows: please contact us.

species_network

The species network topology of the data. Branch lengths are not needed.

mandatory

-gtr

Changes the mutation model from the default JC to GTR.

optional

-allelemap taxaMap

Gene tree / species network taxa association.

optional

-iterations numIterations

The number of hill climbing iterations to use for each run.

optional

-threads numThreads

The number of threads to use when processing.

optional

-numberofruns numRuns

The number of times to restart the hill climbing process.

optional

-noplots

Stop showing plots when finished.

optional

-outputdirectory outputLocation

The directory to store the output of the run.

optional


Examples

 

Command References

  • Liu KJ, Dai J, Truong K, Song Y, Kohn MH, and Nakhleh L (2014) An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. PLoS Comput Biol 10(6): e1003649.

  • Liu KJ, Steinberg E, Yozzo A, Song Y, Kohn MH, and Nakhleh L (2014) Interspecific Introgressive Origin of Genomic Diversity in the House Mouse. Under review. 

See Also

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