Description
Uses a hidden markov to assign a species tree to each loci in data coming from a species network.
Usage
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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 | 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> -treefile "treefile" -outputdirectory "foo" -threads 4 -iterations 300; END; |
Command References
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See Also