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In order to run the PhyloNet toolkit, you must have Java 1.78.0 or later installed on your system. All references to the java command assume that Java 1.7 is being used.
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| Code Block |
|---|
java -jar $PHYLONET_DIRECTORY/PhyloNet_X.Y.Z.jar script.nex |
Where $PHYLONET$PHYLONET_PATH DIRECTORY is the directory of jar file PhyloNet_X.Y.Z.jar, and script.nex is the NEXUS file containing the commands to be executed.
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Add this package to your java library, and load this library before you run PhyloNet.
| Input NEXUS file | Maximum number of reticulations |
|---|---|
| 0 | |
| 1 | |
| 2 | |
| 3 | |
| 4 |
One input example: mcmc_seq.nex
All input NEXUS files: download
Corresponding results: Fig 13 in the book chapter.
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This section corresponds to section 7 in the book chapter.
4.6.1 MDC Inference with unknown hybrid species
| Input NEXUS file | Maximum number of reticulations |
|---|---|
| InferNetwork_MP_0.nex | 0 |
| InferNetwork_MP_1.nex | 1 |
| InferNetwork_MP_2.nex | 2 |
| InferNetwork_MP_3.nex | 3 |
Corresponding results: Fig 17 in the book chapter.
4.6.2 MDC Inference with known hybrid species
| Input NEXUS file | Maximum number of reticulations | Specified hybrid species |
|---|---|---|
| InferNetwork_MP_1.nex | 1 | LPS168 |
| InferNetwork_MP_2.nex | 2 | LPS168 |
| InferNetwork_MP_2_2.nex | 2 | LPS168, LPS189 |
| InferNetwork_MP_3.nex | 3 | LPS168 |
| InferNetwork_MP_3_2.nex | 3 | LPS168, LPS189 |
Corresponding results: Fig 18 in the book chapter.
5. Visualizing a Phylogenetic Network
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