Description
Computes the probabilities of gene tree topologies within a phylogenetic network. The network should have branch lengths, and probabilities associated with reticular edges. Also it must be specified in the Rich Newick Format.
Usage
CalGTProb network_ident (gene_tree_ident1 [, gene_tree_ident2...|, gene_tree_ident2...]) [-a taxa map] [result output file]
network_ident |
The name of the network. |
mandatory |
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gene_tree_ident1 [, gene_tree_ident2...] |
Comma delimited list of gene tree identifiers. |
mandatory |
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-a taxa map |
Gene tree / species tree taxa association. |
optional |
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result output file |
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.
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; CalGTProb net (geneTree1,geneTree2,geneTree3); END;
Command References
- Y. Yu, J.H. Degnan, and L. Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics. 2012.