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;Options file created by: [proftmb];
;----------------------------------;
-d "__pkgdatadir__"
; 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 "proftmb" ; 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
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