-h, --help Print help and exit
--detailed-help Print help, including all details and hidden options, and exit
--full-help Print help, including hidden options, and exit
-V, --version Print version and exit
-s, --seq=\,STRING\/ Sequence file in FASTA format. If the sequence is the first line of the input file, this is not needed (default=`seq.txt')
-p, --previous=\,STRING\/ Previously found LM (output from RNAlocmin or barriers), if specified does not need --seq option
-m, --move=\,STRING\/ Move set: I ==> insertion & deletion of base pairs S ==> I&D& switch of base pairs (possible values="I", "S" default=`I')
-n, --min-num=\,INT\/ Maximal number of local minima returned (0 == unlimited) (default=`100000')
--find-num=\,INT\/ Maximal number of local minima found (default = unlimited - crawl through whole input file)
-v, --verbose-lvl=\,INT\/ Level of verbosity (0 = nothing, 4 = full) WARNING: higher verbose levels increase the computation time (default=`0')
--depth=\,INT\/ Depth of findpath search (higher value increases running time linearly) (default=`10')
--minh=\,DOUBLE\/ Print only minima with energy barrier greater than this (default=`0.0')
--minh-lite When flooding with --minh option, search for only saddle (do not search for a LM that is lower). Increases efficiency a tiny bit, but when turned on, the results may omit some non-shallow minima, especially with higher --minh value. (default=off)
-w, --walk=\,STRING\/ Walking method used D ==> gradient descent F ==> use first found lower energy structure R ==> use random lower energy structure (does not work with --noLP and -m S options) (possible values="D", "F", "R" default=`D')
--noLP Work only with canonical RNA structures (w/o isolated base pairs, cannot be combined with ranodm walk (-w R option) and shift move set (-m S)) (default=off)
-e, --useEOS Use energy_of_structure_pt calculation instead of energy_of_move (slower, it should not affect results) (default=off)
-P, --paramFile=\,STRING\/ Read energy parameters from paramfile, instead of using the default parameter set
-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 is the default for mfe folding but 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 and works only for mfe folding. Note that by default (as well as with -d1 and -d3) pf and mfe folding treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same energy model.--fix-barriers=\,STRING\/ Fix barrier file for interior loops (just recompute if all LM in barrier output are LM), if specified, does not need neither --previous nor --seq option
-k, --pseudoknots Allow for pseudoknots according to "gfold" model - H, K, L, and M types (genus one) of pseudoknots are allowed (increases computation time greatly), cannot be combined with shift move set (-m S) (default=off)
--just-read Do not expect input from stdin, just do postprocessing. (default=off)
-N, --neighborhood Use the Neighborhood routines to perform gradient descend. Cannot be combined with shift move set (-m S) and pseudoknots (-k). Test option. (default=off)
--degeneracy-off Do not deal with degeneracy, select the lexicographically first from the same energy neighbors. (default=off)
--just-output Do not store the minima and optimize, just compute directly minima and output them. Output file can contain duplicates. (default=off)
-b, --bartree Generate an approximate barrier tree. (default=off)
--barr-name=\,STRING\/ Name of barrier tree output file, switches on -b flag. (default=`treeRNAloc.ps')
--barrier-file=\,STRING\/ File for saddle heights between LM (simulates the output format of barriers program)
-r, --rates Create rates for treekin (default=off)
-f, --rates-file=\,STRING\/ File where to write rates, switches on -r flag (default=`rates.out')
-T, --temp=\,DOUBLE\/ Temperature in Celsius (only for rates) (default=`37.0')
--floodPortion=\,DOUBLE\/ Fraction of minima to flood (floods first minima with low number of inwalking sample structures) (0.0 -> no flood; 1.0 -> try to flood all) Usable only with -r or -b options. (default=`0.95')
--floodMax=\,INT\/ Flood cap - how many structures to flood in one basin (default=`1000')
--numIntervals=\,INT\/ Number of intervals for Jing's visualisation (default=`0')
--eRange=\,FLOAT\/ Report only LM, which energy is in range <MFE (or lowest found LM), MFE+eRange> in kcal/mol.
--allegiance=\,STRING\/ Filename where to output the allegiance of structures. Works properly only with RNAsubopt -e list.