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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

Code Block
langhtml
InferSTInfer_ST_MDC_UR {(gene_tree_ident1 [, gene_tree_ident2...]}) [-e proportion] [-x] [-b threshold] [-a taxa map] [-ur] [-t time] [result output file]

gene_tree_ident1 [, gene_tree_ident2...]

Comma delimited set list of gene tree identifiers. See details.

mandatory

-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 thresholdwill 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

...

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

Code Block
langhtml
#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
Code Block
langhtml
#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;

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