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Infers the species tree using the “Minimize Deep Coalescence” (MDC) criterion. The input gene trees must be specified in the rich newick format 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.

The resulting species trees are displayed with the number of extra lineages in each branch. For example, consider the following inferred species tree:

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((a:0,b:0):2,(c:0,d:0):1):0

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

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infer_ST_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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gene_tree_ident1 [, gene_tree_ident2...]
Comma delimited set list of gene tree identifiers. See details.
mandatory
]]></ac:plain-text-body></ac:structured-macro>
-e proportion
Get optimal and sub-optimal trees.
optional
-x
Use all clusters in generation.
optional
-b threshold
Specifies bootstrap threshold. Edges in the gene trees that have support lower than threshold will be contracted.
optional
-a taxa map
Gene tree / species tree taxa association.
optional
-ur
Allow non-binary species tree generation.
optional
-t time
Limit search time to time minutes.
optional
result output file
Optional file destination for command output.
optional
...
Examples
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#NEXUS

BEGIN NETWORKSTREES;

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

END;


BEGIN PHYLONET;

Infer_ST_MDC (g1, g2, g3);

END;
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#NEXUS

BEGIN NETWORKSTREES;

NetworkTree g1 = ((((a1::.550,b1::.550)::.550,c::.550)::.550,d::.550)::.550,e::.550)::.550;
NetworkTree g2 = ((a2::.550,b2::.550)::.550,((c::.550,e::.550)::.550,d::.550)::.550)::.550;
NetworkTree g3 = ((a::.550,c::.550)::.550,((b::.550,e::.550)::.550,d::.550)::.550)::.550;

END;


BEGIN PHYLONET;

Infer_ST_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;

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  • 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