= PHYLOViZ 2.0 =

1. PHYLOViZ is a platform independent JAVA software that allows the analysis
of sequence-based typing methods that generate allelic profiles and their
associated epidemiological data.

2. PHYLOViZ requires Java 7 (or a later version) to be available. We can get
it at https://java.com/en/download/.

3. After download the .zip file available at http://www.phyloviz.com, we
should extract it and run the startup script located in directory bin
according to your operating system.

4. For instance, in Linux you can proceed as follows:

    $ wget https://bitbucket.org/phyloviz/phyloviz-main/downloads/phyloviz-2.0.zip
    $ unzip phyloviz-2.0.zip
    $ cd phyloviz/bin
    $ ./phyloviz

5. In Mac OS X you can also use the same script we used above. In Windows you
can use either phyloviz.exe or phyloviz64.exe.

6. When we are using large datasets we may need to adjust the Java memory
parameters. We can do that by editing the file phyloviz.conf in directory etc
and by changing the variable default_options. We may need to adjust both the
memory allocation pool (option -Xmx) and the thread stack size (option -Xss).

7. As an example, we may adjust the Java memory as follows to increase the
memory allocation pool to 4GB and the thread stack size to 32MB:

    default_options="--branding phyloviz -J-Xss32M -J-Xmx4096M --laf javax.swing.plaf.metal.MetalLookAndFeel"

8. Please let us know about any error or question by filling an issue at
https://bitbucket.org/phyloviz/phyloviz-main/issues

-- PHYLOViZ Team