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PhyloNet is designed, implemented, and maintained by Rice's BioInformatics Group, which is lead by Professor Luay Nakhleh (nakhleh@cs.rice.edu). For more details related to this group please visit http://bioinfo.cs.rice.edu.
This tutorial is based on the book chapter: Practical Aspects of Phylogenetic Network Analysis Using PhyloNet
2. Installation
System Requirements
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| Code Block |
|---|
>java -jar $PHYLONET_PATH PATH/jar/script.nex |
$PHYLONET_PATH is the path of jar file PhyloNet_X.Y.Z.jar
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Where script.nex is the NEXUS file containing the commands to be executed.
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4.1 Inference Under the MDC Criterion
This section corresponds to section 4.1 in the book chapter.
| Input nexus file | Maximum number of reticulations |
|---|---|
| InferNetwork_MP_0_true.nex | 0 |
| InferNetwork_MP_1_true.nex | 1 |
| InferNetwork_MP_2_true.nex | 2 |
| InferNetwork_MP_3_true.nex | 3 |
| InferNetwork_MP_4_true.nex | 4 |
Corresponding results: Fig 4 in section 4.1
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4.2 Maximum Likelihood Inference
| Input nexus file | Maximum number of reticulations |
|---|---|
| InferNetwork_ML_0_true.nex | 0 |
| InferNetwork_ML_1_true.nex | 1 |
| InferNetwork_ML_2_true.nex | 2 |
| InferNetwork_ML_3_true.nex | 3 |
| InferNetwork_ML_4_true.nex | 4 |
Corresponding results: Fig 6.
4.3 Maximum Pseudo-likelihood Inference
| Input nexus file | Maximum number of reticulations |
|---|---|
| InferNetwork_MPL_0_true.nex | 0 |
| InferNetwork_MPL_1_true.nex | 1 |
| InferNetwork_MPL_2_true.nex | 2 |
| InferNetwork_MPL_3_true.nex | 3 |
| InferNetwork_MPL_4_true.nex | 4 |
Corresponding results: Fig 10.
4.4 Bayesian Inference
4.4.1 Bayesian Inference
Input nexus file