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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
| Code Block | ||
|---|---|---|
| ||
DeepCoalCount_network network_ident (gene_tree_ident1 [, gene_tree_ident2...|, gene_tree_ident2...]) [-a taxa map] [-b threshold] [-m ac|mul] [result output fileresultOutputFile] |
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 |
result output fileresultOutputFile | Optional file destination for command output. | optional |
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