Description

Counts the minimum number of extra lineages required to reconcile a list of gene trees within the branches of an allopolyploid network. The species network and gene trees must be specified in the Rich Newick Format.

The input gene trees can be gene tree distributions inferred from Bayesian methods like MrBayes. 

Usage

DeepCoalCount_AlloppNet network_ident (gene_tree_ident1 [, gene_tree_ident2...]) [-a taxa map] [-b threshold][resultOutputFile]

network_ident

The name of the network.

mandatory

gene_tree_ident1 [, gene_tree_ident2...]

Comma delimited list of gene tree identifiers. See details.

mandatory

-a taxa map

Gene tree / species tree taxa association.

optional

-b thresholdSpecifies gene trees bootstrap threshold. Edges in the gene trees that have support lower than threshold will be contracted.optional

resultOutputFile

Optional file destination for command output.

optional

Examples

#NEXUS

BEGIN NETWORKS;

Network net = ((((((X,Y)I5,Z)I4)I7#H1,B)I6,A)I1,(D,(I7#H1,C)I3)I2)I0;

END;


BEGIN TREES;

 
Tree geneTree1 = (((a,b),(x1,y1)),(c,((x2,z2),d)));
Tree geneTree2 = (((((x1,y1),z1),b),a),((((x2,y2),z2),c),d));

END;


BEGIN PHYLONET;

DeepCoalCount_AlloppNet net (geneTree1,geneTree2) -a < A:a; C:c; B:b; D:d; X:x1,x2; Y:y1,y2; Z:z1,z2>;

END;

Command References

See Also