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Sequences and structures are read alternately from stdin. The energy in Kcal/Mol is written to stdout. The program will continue to read new sequences and structures until a line consisting of the single character "@" or an end of file condition is encountered. If the input sequence or structure contains the separator character "&" the program calculates the energy of the co-folding of two RNA strands, where the "&" marks the boundary between the two strands. -h, --help Print help and exit --detailed-help Print help, including all details and hidden options, and exit -V, --version Print version and exit Below are command line options which alter the general behavior of this program --noconv Do not automatically substitude nucleotide "T" with "U" (default=off) -v, --verbose Print out energy contribution of each loop in the structure. (default=off) -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. -4, --noTetra Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (default=off) -d, --dangles=INT How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops (default=`2') With -d1 only unpaired bases can participate in at most one dangling end, this unsupported for the partition function folding. With -d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the default for partition function folding (-p). The option -d0 ignores dangling ends altogether (mostly for debugging). With -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3. -e, --energyModel=INT Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs. -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. -c, --circ Assume a circular (instead of linear) RNA molecule. (default=off) --logML Recalculate energies of structures using a logarithmic energy function for multi-loops before output. (default=off) This option does not effect structure generation, only the energies that are printed out. Since logML lowers energies somewhat, some structures may be missing. References: If you use this program in your work you might want to cite: I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie 125: 167-188 Written by Ivo L Hofacker, Peter F Stadler. Report bugs: If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at. x y$JV0)$ EHYM&$ ADG ACAASN ,JMQP$wJL nD,A,A<BBB B(A0A8JOAG0%AzRx y4JV0T)l$ EHYM& ADG ACA,ADSN $\JMQPwJL nD,A,A4BBB B(A0A8J<OAG0\t%AwIw0U5SUC]CRUR]>\R\5V5RPRV,SRSQsQQ^YYYYUUTQTQQRQRRwwww UVVVUVUVTSSSTSPPPPwwUSwCwU>S>CUPRU`awa{wqvUww UVUVSSw w U ]! ]'T'^! ^QQDQoQQQ Q7 \ Qm | QRR=RoRRR! R7 Z Rm u R0X0V! VYYTYoYYY- Y7 d Ym Y== \ !! \= =_! ! _=8=X8X!8!hXho8oX8X8 X 7 87 d Xd m 8m X 8==VTVT!!aTahYh T m m T X lSSoS m 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 } ? 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