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Phylogenetic network in Rich Newick string can be visualized in Dendroscope or icytree. The former needs downloading, and the latter is online. However, neither can Dendroscope cannot recognize inheritance probabilities (branch lengths are fine), and icytree sometimes can and sometimes cannot. You have need to remove those probabilities manually from the Rich Newick string, or use option "-di" so that PhyloNet returns the network that Dendroscope takes directly. For example, the following network is what PhyloNet returns when the input NEXUS file InferNetwork_MP_ML_pl8_1_true.nex is used:
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((F:12.842,((L:5.576504712905155,((Skud,(Sbay)#H1::O:1.2260000000000002,P:1.2260000000000002)I6:0.36082474226804123),((Spar,Scer),Smik)),#H1:8559999999999997,K:2.082)I2:3.4945047129051554)I0:0.08027116443257487)I8#H1:7.18522412266227::0.63917525773195874334172270375128),Scas),Sklu),Calb);I1:19.128,(I8#H1:1.81722412266227::0.5665827729624873,C:7.474)I4:24.496000000000002)I7; |
After removing "::" and the number after it, we have the network below, which can be visualized in both tools.In order to visualize this phylogenetic network in Dendroscope, please remove the inheritance probabilities like follows, and Dendroscope will be able to read it. Or you can use option "-di".
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((F:12.842,((L:5.576504712905155,((Skud,(Sbay)#H1),((Spar,Scer),Smik)),#H1),Scas),Sklu),Calb)O:1.2260000000000002,P:1.2260000000000002)I6:0.8559999999999997,K:2.082)I2:3.4945047129051554)I0:0.08027116443257487)I8#H1:7.18522412266227)I1:19.128,(I8#H1:1.81722412266227,C:7.474)I4:24.496000000000002)I7; |