Description
Infer the species tree from unrooted gene trees using MDC criterion. The input gene trees must be specified in the Rich Newick Format. Gene trees must be unrooted. The generated output trees will also be generated in the rich newick format.
Usage
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InferSTInfer_ST_MDC_UR {gene_tree_ident1 [, gene_tree_ident2...]} [-e proportion] [-x] [-b threshold] [-a taxa map] [-ur] [-t time] [result output file]
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...
By default, it is assumed that only one individual is sampled per species in gene trees. However, the option -a allows multiple alleles to be sampled.
Examples
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#NEXUS
BEGIN NETWORKS;
Network g1 = ((((a:5,b:5):4,c:9):3,d:12):3,e:15);
Network g2 = ((a:6,b:6):11,((c:12,e:12):2,d:14):3);
Network g3 = ((a:8,c:8):7,((b:14,e:14):1,d:15));
END;
BEGIN PHYLONET;
Infer_ST_MDC_UR (g1, g2, g3);
END
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#NEXUS
BEGIN NETWORKS;
Network g1 = ((((a1::.5,b1::.5)::.5,c::.5)::.5,d::.5)::.5,e::.5)::.5;
Network g2 = ((a2::.5,b2::.5)::.5,((c::.5,e::.5)::.5,d::.5)::.5)::.5;
Network g3 = ((a::.5,c::.5)::.5,((b::.5,e::.5)::.5,d::.5)::.5)::.5;
END;
BEGIN PHYLONET;
InferST_MDC_UR (g1, g2, g3) -b .5 -e .2 -x -ur -t 1 -a <z:a1,a2,a; y:b1,b2,b; c:c; d:d; e:e>;
END;
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Command Refernces
- Y. Yu, T. Warnow, and L. Nakhleh. Algorithms for MDC-based multi-locus phylogeny inference. The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 531--545, 2011. LNBI 6577.
See Also