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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. After unzip the folder, please use -Djava.library.path=YourPath/lib when launching PhyloNet from command line, where YourPath is where the unzipped lib folder is located.
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HmmCommand species_network [-gtr] [-allelemap taxaMap] [-iterations numIterations] [-threads numThreads] [-numberofruns numRuns] [-noplots] [-outputdirectory outputLocation] |
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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> -treefile "treefile" -outputdirectory "foo" -threads 4 -iterations 300;
END;
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