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The algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space. The algorithm furthermore always considers dangle=2 model. -h, --help Print help and exit --detailed-help Print help, including all details and hidden options, and exit -V, --version Print version and exit -c, --cutoff=FLOAT Report only base pairs with an average probability > cutoff in the dot plot (default=`0.01') -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. -4, --noTetra Do not include special stabilizing energies for certain tetra-loops. Mostly for testing. (default=off) --noLP Produce structures without lonely pairs (helices of length 1). (default=off) For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1. --noGU Do not allow GU pairs (default=off) --noClosingGU Do not allow GU pairs at the end of helices (default=off) --noconv Do not automatically substitude nucleotide "T" with "U" (default=off) --nsp=STRING Allow other pairs in addition to the usual AU,GC,and GU pairs. (default=`empty') Its argument is a comma separated list of additionally allowed pairs. If the first character is a "-" then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy. -e, --energyCutoff=INT Energy cutoff or pseudoknot initiation cost. Minimum energy gain of a pseudoknot interaction for it to be returned. Pseudoknots with smaller energy gains are rejected. (default=`-810') -P, --paramFile=paramfile Read energy parameters from paramfile, instead of using the default parameter set. A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format. -v, --verbose print verbose output (default=off) -s, --subopts=INT print suboptimal structures whose energy difference of the pseudoknot to the optimum pseudoknot is smaller than the given value. (default=`0')Author: Wolfgang Beyer Comments should be sent to wolfgang@tbi.univie.ac.at x )$ EHYM&${ADG AgAASN $J^P$:J[@$wJL nD,A,A<BBB B(A0A8JOAG0%AzRx 4)L$d EHYM&{ADG AgA A$SN $<J^P$d:J[@wJL nD,A,A4 BBB B(A0A8JDOAG0d|%AU]U]\\VPV|SSSQmQQYYDYmYUUTQTQQR QRR !w!%w%,w,w CUCV&V'fVftUtyVyUV 5T5S%S'fSfoToSPP$$PPwwUSw'wU"S"'U02U@AwA[wQVU`nwnw `vUvVUVxSSwpwUVpVT^p^Q Q+SQsQQQQ%Q%-Q7FQRR+]RsRRRR%R%-R7?RX\p\Y(Y+iYsYYYY%Y%-Y7fY]](P(]P]P]P]Pp] _ p_8\X\}8}X8X8(X(s8sX8X8X787VXVp82T2TTYssT77_T_fXfpD}SSSsS7Spw wpU S w ' w U V V % R T \ ' \ P S ' S V ' VP T wT w w w w  w " w" $ w$ & w& ( w ( ) w() * w0* 4 w84 w r Ur | r Tr | ? Q? | r Rr ShrRrwS r Xr | ]{]]Uh]]#]R]]] ]*]^] S/S? 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