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• To check your Java version, type "java -version" on your command line. 
• To download Java 1.78, please go to website http://www.java.com/en/download/.
• To link to the new downloaded Java 1.78, for mac, try these two commands from command line: 
  sudo rm /usr/bin/java 
  sudo ln -s /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java /usr/bin

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Acquire the current release of PhyloNet by downloading the most recent version of the PhyloNet JAR file. You will have a file named PhyloNet_X.Y.Z.jar, where X is the major version number and Y and Z are the minor version numbers.

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This section corresponds to section 4.1 in of the book chapter.

4.1.1 MDC Inference using true gene tree topologies

Corresponding results: Fig 4 in the book chapter.

4.1.2 MDC Inference using gene tree topologies estimated by IQTREE

Corresponding results: Fig 5 in the book chapter. 

4.2 Maximum Likelihood Inference

This section corresponds to section 4.2 of the book chapter.

4.2.1 ML Inference using true gene tree topologies

Corresponding results: Fig 6 in the book chapter.

4.2.2 ML Inference using gene tree topologies estimated by IQTREE

Corresponding results: Fig 66 in the book chapter.

4.

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2.3 ML Inference using true gene tree topologies and branch lengths

Corresponding results: Fig 10.

4.4 Bayesian Inference

4.4.1 Bayesian Inference

7 in the book chapter.

4.2.4 ML Inference using gene tree topologies and branch lengths estimated by IQTREE

Corresponding results: Fig 9 in the book chapter.

4.3 Maximum Pseudo-likelihood Inference

This section corresponds to section 4.3 of the book chapter.

4.3.1 MPL Inference using true gene tree topologies

4.3.2 MPL Inference using gene tree topologies estimated by IQTREE

Corresponding results: Fig 10 in the book chapter.

4.4 Bayesian Inference

4.4.1 Bayesian Inference

 Input nexus file