Description
Computes the probabilities of gene tree topologies within a phylogenetic network. The network must be specified in the Rich Newick Format.
Usage
CalGTProb network_ident (gene_tree_ident1 , gene_tree_ident2...) -a taxa map result output file
network_identnt |
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 |
The network should have branch lengths, and probabilities associated with reticular edges.
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 NETWORK; 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 Refernces
- 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.