Compile: make

SADMAMA has many options most of which should be ignored unless you are sure you know what
you're doing. Otherwise stick to the options that are presented in the paper. For example, 
to use the hypergeometric and Mann-Whitney tests:

./sadmama.ukx -w PWMs_file -i1 first_input_set_file -i2 second_input_set_file -t genomic_file_for_model_learning -siteThresholdLearnedFrom 0.001 nullTrainFile -v 0.2 -m 3 -tests freqScoresGTT Hypergeometric + qualityScoresGTT MannWhitney -- -o output_file_name -pwmPC 0.1


To use the bootstrap tests:

./sadmama.ukx -w PWMs_file -i1 first_input_set_file -i2 second_input_set_file -t genomic_file_for_model_learning_and_resampling -siteThresholdLearnedFrom 0.001 nullTrainFile -v 0.2 -m 3 -tests freqScoresGTT MC + qualityScoresGTT MC MC -- -numRandomSets 1000 -set1RandTrainFile _BOTH_ -set2RandTrainFile _BOTH_ -MCmodel bootstrap 10 protectSites -o output_file_name -pwmPC 0.05 





Example of a PWMs_file (you can add many matrices as you like following this format):

>Oriscan (from Breier's gb-2004-5-4-r22-s2.xls)
0.40    0.10    0.07    0.43
0.23    0.07    0.13    0.57
0.33    0.00    0.03    0.63
0.37    0.00    0.10    0.53
0.03    0.00    0.03    0.93
0.13    0.00    0.00    0.87
0.10    0.03    0.00    0.87
0.90    0.03    0.03    0.03
0.07    0.23    0.00    0.70
0.47    0.00    0.47    0.07
0.00    0.00    0.00    1.00
0.00    0.07    0.00    0.93
0.07    0.00    0.00    0.93
0.37    0.00    0.00    0.63
0.03    0.13    0.73    0.10
0.07    0.10    0.17    0.67
0.23    0.07    0.13    0.57
<


Input set files as well as the genomic training file should be in FASTA format.
