...

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.
  
  

HmmCommand species_network [-gtr] [-allelemap taxaMap]  [-iterations numIterations] [-threads numThreads] [-numberofruns numRuns] [-noplots] [-outputdirectory outputLocation]

...

#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

• 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. 

• Y. Yu, R.M. Barnett, and L. Nakhleh. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology, vol. 62, no. 5, pp. 738-751, 2013.
• Y. Yu, N. Ristic and L. Nakhleh. Fast algorithms and Heuristics for Phylogenomics under hybridization and incomplete lineage sorting.  BMC Bioinformatics, vol. 14, no. Suppl 15, p. S6, 2013.
• Y. Yu, J. Dong, K. Liu, and L. Nakhleh, Probabilistic inference of reticulate evolutionary histories, Under Review.

See Also

• List of PhyloNet Commands