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• To check your Java version, type "java -version" on your command line. 
• To download Java 1.8, please go to website http://www.java.com/en/download/.

• To link to the new downloaded Java 1.8, for mac, try these two commands from command line: 

  Code Block
  sudo rm /usr/bin/

  java 
  

  java sudo ln -s /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java /usr/bin

Downloading phylonet.jar

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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Place the jar file in the desired installation directory. The remainder of this document assumes that it is located in directory $PHYLONET_PATHDIRECTORY. 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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The PhyloNet tool is executed by typing the following command into your console:

>javajava -jar $PHYLONET_PATHDIRECTORY/PhyloNet_X.Y.Z.jar script.nex

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