• DeepCoalCount_network
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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

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 mulSpecify the algorithm used for computation (see reference). The default value is ac.optional

-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

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

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.

See Also

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