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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.