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The species network and gene trees must be specified in the Rich Newick Format. The branch lengths and the inheritance probabilities in the species network need to be specified. Only topologies of gene trees are used in the method.
Usage
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CalIntroRate network geneTreeList |
network | The name of the network. | mandatory |
geneTreeList | Comma delimited list of gene tree identifiers or comma delimited list of sets of gene tree identifiers. See details. | mandatory |
Examples
#NEXUS BEGIN NETWORKS; Network net = ((((R:1.0)I12#H1:1.0::0.79)I10#H2:1.0::0.52,(((Q:1.0,I12#H1:1.0::0.21)I11:5.94,((A:1.0,(C:1.0,G:1.0)I5:1.00)I4:0.92)I6#H3:1.13::0.97)I3:0.91,(L:1.0,I10#H2:1.0::0.48)I9:0.33)I2:5.94)I1:0.84,I6#H3:0.01::0.03)I0; END;
Tree geneTree1 = ((L,R),(Q,(A,(G,C)))); END;
CalIntroRate net ({geneTree1,geneTree2,geneTree3}); END; |
#NEXUS BEGIN NETWORKS; Network net = ((((R:1.0)I12#H1:1.0::0.79)I10#H2:1.0::0.52,(((Q:1.0,I12#H1:1.0::0.21)I11:5.94,((A:1.0,(C:1.0,G:1.0)I5:1.00)I4:0.92)I6#H3:1.13::0.97)I3:0.91,(L:1.0,I10#H2:1.0::0.48)I9:0.33)I2:5.94)I1:0.84,I6#H3:0.01::0.03)I0; END;
Tree geneTree1 = ((L,R),(Q,(A,(G,C)))); END;
CalIntroRate net (geneTree1,geneTree2,geneTree3); END; |
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