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Computes the probabilities of gene tree topologies within a phylogenetic network. The network must be specified in the Rich Newick Format.
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Usage
CalGTProb network_ident (gene_tree_ident1 , gene_tree_ident2...) -a taxa map result output file
network_identnt | The name of the network. | mandatory | ||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="567da4f73512287c-0e0c345a-4de440a6-b82abfcf-ff1736955c85e207c0736979"><ac:plain-text-body><![CDATA[ | gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited list of gene tree identifiers. | mandatory | ]]></ac:plain-text-body></ac:structured-macro> |
-a taxa map | Gene tree / species tree taxa association\. | optional | ||
result output file | Optional file destination for command output. | optional |
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| Wiki Markup |
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By default, it is assumed that only one individual is sampled per species in gene trees. However, the option {{\[-a}} [taxa map|confluence/display/PHYLONET/Taxa+Map+Command+Parameter]{{\]}} allows multiple alleles to be sampled. |
Examples#NEXUS
BEGIN NETWORK;
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Examples
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#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); |
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END; |
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BEGIN TREES; |
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Tree geneTree1 = (C,((B,D),A)); |
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Tree geneTree2 = (B,(D,(C,A))); |
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Tree geneTree3 = (D,(B,(C,A))); |
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END; |
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BEGIN PHYLONET; |
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CalGTProb net (geneTree1,geneTree2,geneTree3) |
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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.