**-cv***factor*- Set the weight of the covariance term in the energy function to
*factor*. Default is 1. **-nc***factor*- Set the penalty for non-compatible sequences in the covariance
term of the energy function to
*factor*. Default is 1. **-E**- Score pairs with endgaps same as gap-gap pairs.
**-mis**- Output "most informative sequence" instead of simple consensus: For each column of the alignment output the set of nucleotides with frequency greater than average in IUPAC notation.
**-p**- Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only. Additionally, the centroid structure is computed and printed out.
**-MEA***[gamma]*- Calculate an MEA (maximum expected accuracy) structure. See RNAfold man page for details. If gamma is not specified a default of gamma=1 is used. Using -MEA implies -p.
**-noLP**- Avoid structures without lonely pairs (helices of length 1). In
the mfe case structures with lonely pairs are strictly forbidden.
For partition function folding this disallows pairs that can
**only**occur isolated. Setting this option provides a significant speedup. **-circ**- Assume circular (instead of linear) RNA molecules.
**-color**- Produce a colored version of the consensus structure plot "alirna.ps" (default b&w only).
**-aln**- Produce a colored and structure annotated alignment in PostScript format in the file "aln.ps" in the current directory.
**-s***num*- Compute a stochastic sample of
*num*random structures chosen according to their Boltzmann probability. See the -p option in RNAsubopt. **-se***num*- like
**-s**, but also print out the energy and probability of each structure in the sample. **-R***Ribosum_Matrix*- use specified Ribosum Matrix instead of normal energy model. Matrices to use should be 6x6 matrices, the order of the terms is AU, CG, GC, GU, UA, UG.
**-r**- use Ribosum scoring matrix. The matrix is chosen according to the minimal and maximal pairwise identities of the sequences in the file. When using Ribosum scores, best benchmark results were achieved with options -cv 0.6 -nc 0.5 (see above).
**-old**- use old energy evaluation, treating gaps as characters.

The **-T**, **-d**, **-4**, **-noGU**,
**-noCloseGU**, **-e**, **-P**, **-nsp**, options
should work as in RNAfold

If using **-C** constraints will be read from stdin, the
alignment has to given as a file name on the command line.

D.H. Mathews, J. Sabina, M. Zuker and H. Turner "Expanded Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure" JMB, 288, pp 911-940, 1999

If you use this program in your work you might want to cite:

Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler "Secondary
Structure Prediction for Aligned RNA Sequences". J.Mol.Biol. 319:
1059-1066, 2002.

Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R.
Gruber, and Peter F. Stadler. "RNAalifold: Improved consensus
structure prediction for RNA alignments". BMC Bioinformatics,
9:474, 2008

Comments should be sent to rna@tbi.univie.ac.at.

This document was created by man2html, using the manual pages.

Time: 07:19:16 GMT, February 23, 2011