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
| Code Block | ||
|---|---|---|
| ||
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 threshold | Specifies 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
| Code Block | ||
|---|---|---|
| ||
#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
- Yan, Z., Cao, Z., Liu, Y., and Nakhleh, L. Species Network Inference in the Presence of Polyploid Complexes Using PhyloNet. Manuscript in preparation.
Yu, Y., Barnett, R., and Nakhleh, L. 2013. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology, 62(5): 738–751.