Description

Infer the species tree using MDC criterion but considering time. The input gene trees must be specified in the Rich Newick Format. Gene trees must be rooted and have branch length. 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

inferSTinfer_ST_MDC_TIME {gene_tree_ident1 [, gene_tree_ident2...]} [-b threshold] [-a taxa map] [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: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;

InferSTInfer_ST_MDC_Time (g1, g2, g3);

END;

See Also

• List of PhyloNet Commands