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.
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HmmCommand species_network [-gtr] [-allelemap taxaMap] [-iterations numIterations] [-threads numThreads] [-numberofruns numRuns] [-noplots] [-outputdirectory outputLocation] |
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
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#NEXUS
BEGIN NETWORKS;
Network net = ((A:3,ANC#H1:2.25):2,((B:.75)ANC#H1:0,C:.75):4.25);
END;
Begin DATA;
dimensions ntax=3 nchar=6;
format datatype=dna symbols="ACTG" missing=? gap=-;
matrix
1 AGGTGG
2 AACCTT
3 ACCTGT
;
END;
BEGIN PHYLONET;
HmmCommand net -allelemap <A:1; B:2; C:3> -outputdirectory "foo" -threads 4 -iterations 300;
END;
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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.