DNA/AA sequence simulator that uses the Halpern and Bruno 1998 model of evolution
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README

This project contains modifications to the source code for the BULL simulator
    used in:
    
        Holder, Zwickl, and Dessimoz. "Evaluating the robustness of phylogenetic
            methods to among-site variability in substitution processes."
            Philos Trans R Soc Lond, B, Biol Sci (2008) 4013-4021


Most of the code was by Mark Holder or Tracy Heath.

All of Mark Holder's code contributions to Bull are released under the GNU
    Public License.
 
Some code (as noted in the code) was taken from MrBayes (John Huelsenbeck and
    Fredrik Ronquist), PAML (Ziheng Yang), and NCL (Paul Lewis). Some of the 
    code derived MrBayes was originally written by David Swofford.
       

Compilation:
    1. download and install NCL version 2.1.
    2. set an env variable to the absolute path of the location that you used
        as a prefix to NCL's configure (by default the prefix is /usr/local). 
        Call this variable NCL_INSTALL_PREFIX (it is used in the configure
        invocation of bullSim below).
    3. download and install autotools (autoconf and automake).
    4. from the top of the bullSim directory do the following:

$ mkdir build
$ sh bootstrap.sh
$ cd build
$ ../configure --prefix=`pwd`/installed --with-ncl=$NCL_INSTALL_PREFIX/installed
$ make
$ make install

To run the example simulation file, then use:

$ ./installed/bin/bullSim ../test/cytb-sim.nex



Usage:
    bullSim <file name> 
    
See the BULL block in test/cytb-sim.nex for the syntax of the simulation command.

Note that the code in src/oldsrc is a modified a version of the code used for 
    ML inference of the parameters for the cytochrome b (it has been a while since
    this code was used or tested, so it is possible that it will take some
    work to resurrect the inference functionality).