The BRAT NextGen page

This page contains information about the BRAT NextGen software for Bayesian analysis of recombinations in whole-genome DNA sequence data, which is available for Windows, Linux and Mac OS X operative systems.

For Mac, the two zip-archives contain executables and script files to set up paths for OS X. "bratPermutationRun.zip" is the separate executable for running permutation tests in parallel on different computers. For installation, please follow the instructions available for installing BAPS 5.4 , and simply replace the following part in the X11 command

./run_baps5.sh

by

./run_bratNextGen.sh

when using the main program. To run the separate executable you need to provide the following 3 input arguments to the shell script run_bratPermutationRun.sh : 1) the indices of permutation runs done on any single computer, 2) full path to the .mat file saved in the main program, 3) full path to a folder where permutation run results will be stored (see manual for details). The manual contains examples of paths for Windows, below we provide an example for the corresponding X11 command:

./run_bratPermutationRun.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ 10 /Users/jukkasmac/Desktop/bratResults/testresults.mat /Users/jukkasmac/Desktop/bratResults/permutationResults

where you should replace 'jukkasmac' by your own computer name and the folder names with those present on your system. Here 'testresults.mat' is a result file saved within a session on the main program and 'permutationResult's is a folder where the results will be saved using the specified output file index value (equals '10' in this example). Note that all specified folders must be created before launching the executable.

NB X11 commands are case-sensitive so ensure that the file and folder names are correctly spelled should you receive the error message 'no such file or folder' Ensure also that you entered a space between each input argument.

Notice that before BRAT is functional you need to install the MCR runtime component using the .dmg installer file in the BAPS 5.4 package (see here)!