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caozhen-bupt authored Mar 4, 2022
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## Installation
1. To download the binary java package directly, you can click
[PhyloNet.jar](https://github.com/NakhlehLab/PhyloNet/releases/latest/download/PhyloNet.jar)
[PhyloNet.jar](https://github.com/NakhlehLab/PhyloNet/releases/latest/download/PhyloNet.jar).

2. To download the source code and build by yourself, you can clone the repo and use command "ant"
2. To download the source code and build by yourself, you can clone the repo and use command "ant".

## Usage
The basic usage is java -jar PhyloNet.jar name.nex
* [PhyloNet homepage](https://bioinfocs.rice.edu/phylonet)
The basic usage is java -jar PhyloNet.jar name.nex.
* [PhyloNet homepage](https://bioinfocs.rice.edu/phylonet).
* [General overview](https://wiki.rice.edu/confluence/display/PHYLONET/PhyloNet+3+General+Overview) for installation, basic usage, input and output examples.
* [List of PhyloNet commands](https://wiki.rice.edu/confluence/display/PHYLONET/List+of+PhyloNet+Commands) for preparing nexus files for command.
* [PhyloNet tutorial](https://wiki.rice.edu/confluence/pages/viewpage.action?pageId=39500205) for input nexus file examples of phylogenetic network inference.

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