General Options:

Below are command line options which alter the general behavior of this program

-v, --verbose

Be verbose (default=off)

Repulsive Sampling Options:

--sequence=STRING

Input sequence (default=`')

--penalize-structures

Penalize structures instead of base pairs of local minima, that occure too often. (default=off)

--struc1=STRING

Input structure 1 (default=`')

--struc2=STRING

Input structure 2 (default=`')

--granularity=INT

Granularity, i.e. number of samples after which distortion checks are performed (default=`100')

-n, --num-samples=INT

Number of samples in total. The number of samples per iteration is n/g. (default=`100000')

-f, --exploration-factor=FLOAT

Exploration factor (default=`1')

--min-exploration-percent=FLOAT

Minimum exploration percentage before adding

new repelled structures

(default=`1')

--cluster

Cluster resulting local minima to reduce effective size (default=off)

--lmin-file=STRING

Output filename for local minima (default=`')

--TwoD-file=STRING

Output filename for pseudo-2D file (default=`')

--nonred

Do sampling with non-redundant pbacktrack (default=off)

--nonred-file=STRING

Input filename for nonredundant samples (default=`')

-2, --explore-two-neighborhood

Explore 2-Neighborhood of local minima, i.e.

eliminate shallow minima

(default=off)

--post-filter-two

Post processing Filter local minima according to 2-Neighborhood, i.e. eliminate shallow minima (default=off)

--ediff-penalty

Use energy difference instead of kT for penalty (default=off)

--mu=FLOAT

proportion factor used to decide whether sampling round was sufficient (default=`0.1')

Algorithms:

Select additional algorithms which should be included in the calculations. Default is the repellant sampling heuristic. Display more options with --detailed-help.

-M, --method=<method>

Set the method used to obtain meshpoint structures for the bisection algorithm

(default=`RSH')

Available options are:

GW

Gradient Walk (default)

MC

Monte Carlo walk

MC-SA

Monte Carlo Walk

with simulated Annealing

DB-MFE

Distance based MFE structure

meshpoints

TRATES

Transition rate computation

SM

Stochastic sampling method with 2D mapping (activate distortion

with -e"N").

RS

Repellant or Attraction sampling

RSH

Repellant sampling heuristic

RL

Retrieve local minima. Standard input should be a sequence and a

set of secondary structures (one per line). \

--betaScale=DOUBLE

Set the scaling of the Boltzmann factors (default=`1.')

The argument provided with this option enables to scale the thermodynamic temperature used in the Boltzmann factors independently from the temperature used to scale the individual energy contributions of the loop types. The Boltzmann factors then become exp(-dG/(kT*betaScale)) where k is the Boltzmann constant, dG the free energy contribution of the state and T the absolute temperature.

-e, --extended_opt=STRING

Some extended options: N normal distortion (no shift) B alter both potentials at once R relax potential instead of increasing it S shift potential to other structure F shift to first structure V verbose

(default=`')

-i, --iterations=INT

Set the number of iterations/simulations

(default=`1')

-m, --maxKeep=INT

maxKeep for direct path search

(default=`10')

-s, --maxStore=INT

amount of best solutions to hold per iteration

(default=`10')

-r, --remember=INT

Set the number of structure states to remember in a TABU list

(default=`10')

-c, --circ

Assume a circular (instead of linear) RNA molecule.

(default=off)

--cooling-rate=FLOAT

Cooling factor used for simulated annealing

(default=`0.9998')

--tstart=FLOAT

start temperature in deg. Celcius

(default=`37.0')

--tstop=FLOAT

stop temperature in deg. Celcius

(default=`0.0')

--penalizeBackWalks

Add a penalty for backward moves, i.e. moves along states already visited

(default=off)

--basinStructure

just perform a gradient walk starting from a given structure

(default=off)

-D, --maxD=INT

Maximum base pair distance between meshpoints and references

(default=`5')

--maxD1=INT

Maximum base pair distance between meshpoints and reference structure 1

(default=`5')

--maxD2=INT

Maximum base pair distance between meshpoints and reference structure 2

(default=`5')

Model Details`:

-T, --temp=DOUBLE

Rescale energy parameters to a temperature of temp C. Default is 37C.

--p0=STRING

Set the percentage of the references distortion value <int> to <double> Can be given for all reference indices (NOTE: the value <double> should be between 0 and 1) (example: "--p0 2=0.5" - distortion value of sequence 2 will be multiplied with 0.5 before sampling.)

Gradient walker options`:

--shift_moves

Use shift moves for gradient walks.

(default=off)

-P, --parameter_file=STRING

Use the given parameter file for gradient walks.