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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; BEGIN TREES; Tree geneTree1 = ((L,R),(Q,(A,(G,C)))); Tree geneTree2 = (R,(L,(A,(Q,(G,C))))); Tree geneTree3 = (R,(L,(Q,(G,(A,C))))); END; BEGIN PHYLONET; 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; BEGIN TREES; Tree geneTree1 = ((L,R),(Q,(A,(G,C)))); Tree geneTree2 = (R,(L,(A,(Q,(G,C))))); Tree geneTree3 = (R,(L,(Q,(G,(A,C))))); END; BEGIN PHYLONET; CalIntroRate net (geneTree1,geneTree2,geneTree3); END;

 

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