Description
Counts the minimum number of extra lineages required to reconcile a list of gene trees within the branches of a phylogenetic 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_network network_ident (gene_tree_ident1 [, gene_tree_ident2...]) [-a taxa map] [-b threshold] [-m ac|mul] [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 |
| -m ac or mul | Specify the algorithm used for computation (see reference). The default value is ac. | optional |
-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 |
By default, it is assumed that only one individual is sampled per species in gene trees. However, the option [-a taxa map] allows multiple alleles to be sampled.
The -m option is used to specify the algorithm for computation, where mul stands for the algorithm based on MUL-trees (Yu Et. Al, under review) and ac stands for the algorithm based on ancestral configurations (Yu and Nakhleh, under review). They produce exactly the same result, but the latter one is more efficiently in general cases.
Examples
#NEXUS BEGIN NETWORKS; Network net = ((A:2,((B:1,C:1):1)X#H1:0::0.3):1,(D:2,X#H1:0::0.7):1); END; BEGIN TREES; Tree geneTree1 = (C,((B,D),A)); Tree geneTree2 = (B,(D,(C,A))); Tree geneTree3 = (D,(B,(C,A))); END; BEGIN PHYLONET; DeepCoalCount_network net (geneTree1,geneTree2,geneTree3); END;
Command References
- Y. Yu, R.M. Barnett, and L. Nakhleh. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Under review.
- Y. Yu and L. Nakhleh. Fast algorithms for reconciliation under hybridization and incomplete lineage sorting. Under review.