# Introduction
Beagle_optimiser is a program written in Python 
that takes an XML input file prepared for BEAST, and 
finds the beagle option that will result in the 
shortest analysis time of that file. You can find out 
more about the program in the open laboratory notebook
at http://matstopel.se/notebook/beagle-optimiser.



# The program has the following functions:

mats@Slartibartfasts:~/project/beagle/test$ ./beagle_optimiser_0.9 -h

Usage: 
beagle_optimiser_0.9.2 [-r] [-q] [-d] [--nogpu] [-f] FILE [-t] NAME [-n] N -i [file1 file2 ..]

Options:
--version               Show program's version number and exit.
-h, --hele              Show this help message and exit.
-q, --quiet             Minimum or no output to STDOUT.
-r, --run               Run beast with the best speed settings immediately
                        after the test.
-f FILE, --file=FILE    Write output to FILE [bo_output.txt].
-t NAME, --tmpdir=NAME
                        Name of temporary directory for output files. This
                        directory will be removed after the beagle tests are
                        done if the --dev flag was not invoked [.bss_tmp].
-n N, --ngen=N          Chainlength for the Beast runs [10000].
--nogpu                 Do not use the "-Beagle_GPU" flag in the test.
-d, --dev               Produce more output to STDOUT and save all temporary
                        files.
-i, --input             Followed by one or several input files.



# Output from the program looks like this:
_______________________________________

File: benchmark1.xml
Sequences: 1441
Sites: 987
Unique patterns: 593
_______________________________________

Beast option:         Time:

-beagle_SSE           199.66 seconds
-beagle_CPU           204.72 seconds
-beagle_instances 2   211.04 seconds
-beagle_instances 10  223.12 seconds
-beagle_instances 8   227.52 seconds
-beagle_instances 4   233.74 seconds
-beagle_instances 12  237.6 seconds
-beagle_instances 16  245.73 seconds
-beagle_instances 14  253.28 seconds
-beagle_GPU           263.08 seconds
 Native library       386.7 seconds
-java                 389.06 seconds
 _______________________________________



# TODO
Use a random seed when the "-r" option is used.
Make BO work with MrBayes 3.2
Test different beagle options in combination (is that relevant?)