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Place the jar file in the desired installation directory. The remainder of this document assumes that it is located in in directory $PHYLONET_PATH/jar. Installation is now complete. In order to run PhyloNet, you must execute the file PhyloNet_X.Y.Z.jar, as described in the next section.

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>java -jar $PHYLONET_PATH/PhyloNet_X.Y.Z.jar script.nex

Where $PHYLONET_PATH is the path directory of jar file PhyloNet_X.Y.Z.jar.Where , and script.nex is the NEXUS file containing the commands to be executed.

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Here we provide all the input nexus files in section 4 of the book chapter. The figure below is the true network we would like to infer. You can also find all the commands below on https://wiki.rice.edu/confluence/display/PHYLONET/List+of+PhyloNet+Commands .

 4.1 Minimize deep coalescent Inference

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4.1.1 MDC Inference using true gene tree topologies

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4.1.2 MDC Inference using gene tree topologies estimated by IQTREE

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4.2.1 ML Inference using true gene tree topologies

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4.2.2 ML Inference using gene tree topologies estimated by IQTREE

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4.2.3 ML Inference using true gene tree topologies and branch lengths

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

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4.3.1 MPL Inference using true gene tree topologies

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4.3.2 MPL Inference using gene tree topologies estimated by IQTREE

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4.3.3 MPL Inference using bi-allelic marker data

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4.4.1 MCMC_SEQ: Bayesian inference on the sequence alignment data

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4.4.2.1 MCMC_GT sampling using true gene tree topologies

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4.4.2.2 MCMC_GT sampling using gene tree topologies estimated by IQTREE

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4.4.3 MCMC_BiMarkers: Bayesian inference on the bi-allelic markers

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