| ## RNAstructure Command Line Help AlignmentFold and AlignmentFold-smp | ### Contents ### Index
AlignmentFold is used to predict the lowest free energy structure and a set of suboptimal structures, i.e. low free energy structures, for a structure conserved in a set of aligned homologs. AlignmentFold-smp is the parallel version for use on multi-core computers. ### USAGE: AlignmentFold <alignment file> <CT file> [options] ### OR: AlignmentFold-smp <seq file> <ct file> [options] ### Required parameters:
<alignment file> | The name of an inputfile containing multiple sequence alignment of homologous RNA sequences in FASTA format.
<ct file> | The name of a CT file to which output will be written. The CT file will show the first sequence of the input alignment. If the --bracket flag is present, output will be written as a dot-bracket file. If the file name is a hyphen (-), the structure will be written to standard output (STDOUT) instead of a file.
### Options that do not require added values:
--disablecoax | Specify that coaxial stacking recusions should not be used. This option uses a less realistic energy function in exchange for a faster calculation.
-h, --help | Display the usage details message.
-k, --bracket | Write the predicted structure in dot-bracket notation (DBN) instead of CT format.
-mfe, -MFE, --MFE | Specify that only the minimum free energy structure is needed. No savefiles can be generated. This saves nearly half the calculation time, but provides less information.
-q, --quite | Suppress unnecessary output. This option is implied when the output file is '-' (STDOUT).
-v, --version | Display version and copyright information for this interface.

### Options that require added values:

-b, -B, --bpcutoff | Specify the base pairing cutoff. Default is 0.3
-l, -L, --loop | Specify a maximum internal/bulge loop size. Default is 40 unpaired nucleotides.
-m -M --maximum | Specify a maximum number of structures. Default is 20 structures.
-p -P --percent | Specify a maximum percent energy difference. Default is 10 percent (specified as 10, not 0.1).
-s -S --save | Specify the name of a save file, needed for dotplots and refolding. Default is not to generate a save file.
-w -W --window | Specify a window size. Default is determined by the length of the sequence.

### Notes for smp:

AlignmentFold-smp, by default, will use all available compute cores for processing. The number of cores used can be controlled by setting the OMP_NUM_THREADS environment variable.

### References:

1. Reuter, J.S. and Mathews, D.H.
   "RNAstructure: software for RNA secondary structure prediction and analysis."
   BMC Bioinformatics, 11:129. (2010).