ct-cbn :: Continuous time conjunctive Bayesian networks ------------------------------------------------------- -- Version 0.1.01, Apr 2009 Prerequisites: -------------- Version 0.1.01 requires the GNU Scientific Library (GSL), which is freely available at: http://www.gnu.org/software/gsl/ Openmp parallelization requires gcc v. 4.2+. Installation: ------------- - Decompress and unpack files in a separate directory. - Make sure the paths to GSL in the Makefile are correct. - Type 'make' to compile the executables 'ct-cbn' and 'h-cbn' Description: ------------ 'ct-cbn' is an implementation of the continuous time conjunctive Bayesian network as described in Beerenwikel & Sullivant, http://arxiv.org/abs/0709.2646v1. 'h-cbn' is a more recent implementation of the CBN with an explicit error process. Usage: ------ Type 'ct-cbn -h' or 'h-cbn -h' for available options. File formats: ------------- (a) Pattern files (.pat): A binary data matrix preceeded by its dimensions (#rows #columns) in the first line. The initial event (column 1) must always occur, i.e., all patterns have to start with a 1 followed by a space-separated list of 0's and 1's. Note that the pattern matrix is not checked for validity! Example with 7 mutations: 10 8 1 0 0 0 1 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 0 0 1 1 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 1 1 0 1 0 1 1 (b) Poset files (.poset): A list of binary relations preceeded by the number of genetic events (mutations). A relation "i