Description

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

Usage

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

Species network taxa association.optional
-iterations numIterationsThe number of hill climbing iterations to use for each run.optional
-threads numThreadsThe 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 outputLocationThe directory to store the output of the run.optional

 

 

Examples

#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;

 

Command References

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See Also

 


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