;Options file created by: [proftmb];
;----------------------------------;
-d "."                               
                    ; root path where files (options
                    ; -s,-r,-l,-a,-e,-t,-u,-z,-n) reside
                    ; -d == --directory-root
-a "StateRedux4"                     ; state reduction for decoding
                                     ; -a == --reduction-state-decode
-b "ReduxDecode4"                    ; state reduction for reporting
                                     ; -b == --reduction-state-report
-m "StrandStates"                    ; list of membrane strand states
                                     ; -m == --membrane-strand-states
-z "Swiss_Zcurve"                    
                    ; file containing means and sd's at integral length
                    ; values
                    ; -z == --z-curve-file
-x "ZCalibration"                    
                    ; file mapping coverage and accuracy values to z-scores
                    ; -x == --z-calibration-curve
-n "bact.comp"                       ; background frequency file
                                     ; -n == --null-frequency
-c 4                                 
                    ; minimum z-score for per-residue prediction
                    ; -c == --minimum-score-cutoff
-o ""                                ; output file prefix
                                     ; -o == --outfile-prefix
-s "Swiss8.arch"                     
                    ; data representing the model architecture
                    ; -s == --static-model-data
-t "Swiss8.params"                   
                    ; params representing the encoded training data
                    ; -t == --trained-params
-q ""                                
                    ; psiblast directory (full pathname or relative to
                    ; current directory) with many profiles
                    ; -q == --test-blastQ-dir
-v ""                                
                    ; list of mappings of filename to protein name
                    ; -v == --list-blastQ-files