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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).