...
network_identnt | The name of the network. | mandatory | ||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="da55ba8ed229644b-6b63a636-474d4b9a-9741967f-1cabb7459db9435f9c37a9a9"><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|confluence/display/PHYLONET/Taxa+Map+Command+Parameter\. | optional | ||
result output file | Optional file destination for command output. | optional |
...
Wiki Markup |
---|
By default, it is assumed that only one individual is sampled per species in gene trees. However, the option {{\[-a}} {{[_taxa map_|Taxa Map Command Parameter]}}{{\]}} allows multiple alleles to be sampled. |
...
Code Block | ||
---|---|---|
| ||
#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.
...