NAME

       RNAlocmin - manual page for RNAlocmin 2.1.0

SYNOPSIS

       RNAlocmin [OPTIONS]... [FILES]...

DESCRIPTION

       RNAlocmin 2.1.0

   Calculate local minima from structures via gradient walks. Example usage:
              RNAsubopt  -p  10000  <  "sequence.txt"  >  "suboptp.txt"  RNAlocmin -s "sequence.txt" [OPTIONS] <
              "suboptp.txt"

       -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

   General options:
       -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)

   Barrier tree:
       -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')

   Kinetics (rates for treekin program):
       --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')

   Flooding parameters (flooding occurs only with -r, -b, or --minh option):
       --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')

   Miscelaneous:
       --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.

RNAlocmin 2.1.0                                     July 2017                                       RNALOCMIN(1)