Phylo-SMC

Installation instructions

Make sure the following tools are installed and available in the PATH variable: (for each item in the list below, we show in bracket which commands in this distribution need this item---see the usage page for a description of the commands.)

• Java 1.5+ (Sun/Oracle's version). [all] Typing 'java -version' should show the version and contain the word 'HotSpot'. Download from java.com
• Phylip 3.69. [run-rna.bash; run-synthetic.bash] Used for creating a binary consensus tree in the current release. Typing 'which neighbor' should give a path to the executable. Can be downloaded from http://evolution.genetics.washington.edu/phylip/executables.html. Make sure the subfolder exe is in the path.
• Mrbayes-3.1.2. [run-rna.bash; run-synthetic.bash] Used to compare SMC against MCMC. Typing 'which mb' should give a path to the executable (for mac users, download the unix source version and compile using x-code to make sure you have access to the command line version of the tool). Download from http://mrbayes.sourceforge.net/
• R stat package. [create-figures.bash] For creating plots. Typing 'which r' (in small caps) should give a path to the executable. Can be downloaded from www.r-project.org/

You can now use the software, see the instructions for using the software: [html].