;Options file created by: [proftmb];
;----------------------------------;
-d "."                               
                    ; root path where files (options
                    ; -s,-r,-l,-a,-e,-t,-u,-z,-n) reside
                    ; -d == --directory-root
-s "TrainingSeqsOnly"                ; labelled training sequence file
                                     ; -s == --sequence-file
-f "TrainingLabels"                  ; sequence label file
                                     ; -f == --sequence-label-file
-r "Architecture"                    ; architecture file
                                     ; -r == --arch-file
-l "Label2Label"                     ; label-to-label file
                                     ; -l == --label2label-map
-a "Label2Arch"                      ; label-to-arch file
                                     ; -a == --label2arch-map
-e "TiedStates"                      ; arch-to-emission file
                                     ; -e == --arch-map
-t "StateRedux4"                     ; state reduction for decoding
                                     ; -t == --reduction-state-decode
-u "ReduxDecode4"                    ; state reduction for reporting
                                     ; -u == --reduction-state-report
-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
-q ""                                
                    ; psiblast profile (-Q) or directory (full pathname or
                    ; relative to current directory) with many profiles
                    ; -q == --test-blastQ-file-or-dir
-v ""                                
                    ; list of psiblast files to process in directory (leave
                    ; blank to process all files)
                    ; -v == --list-blastQ-files
-b 4                                 
                    ; minimum z-score for per-residue prediction
                    ; -b == --minimum-score-cutoff
-o "recent_test"                     ; output file prefix
                                     ; -o == --outfile-prefix
-p ""                                
                    ; dirichlet mixture file, no regularization if blank
                    ; -p == --dirichlet-prior