Description

Infers the species tree using the “Minimize Deep Coalescence” (MDC) criterion. The input gene trees must be specified in the Rich Newick Format. Gene trees must be rooted. Gene losses are allowed. The generated output trees will also be generated in the rich newick format.

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In this species tree, there are two extra lineages in branch between node (a, b) and the root, and one extra lineage in branch between node (c, d) and the root. All other branches have 0 extra lineages.

Usage

inferST_MDC {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

#NEXUS

BEGIN NETWORKS;

Network g1 = ((((a,b),c),d),e);
Network g2 = ((a,b),((c,e),d));
Network g3 = ((a,c),((b,e),d));

END;


BEGIN PHYLONET;

Infer_ST_MDC (g1, g2, g3);

END;

#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 (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;

Command Refernces

• C. Than and L. Nakhleh. Species tree inference by minimizing deep coalescences. PLoS Computational Biology, 5(9):e1000501, 2009.

• Y. Yu, T. Warnow, and L. Nakhleh, "Algorithms for MDC-based multi-locus phylogeny inference." Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), LNBI 6577, 531-545, 2011.

• Y. Yu, T. Warnow, and L. Nakhleh, "Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles." Journal of Computational Biology, 18(11): 1-18, 2011.

See Also

• List of PhyloNet Commands