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RNAstructure Command Line Help

phmm uses a pairwise hidden markov model (HMM) to predict the alignment between two RNA sequences. The default behavior is to produce a matrix of alignment probabilities. It can also produce maximum likelihood alignment calculated using the Viterbi algorithm.

USAGE: phmm <sequence file 1> <sequence file 2> <output file> [options]

Required parameters:

<sequence file 1> The name of a sequence file containing input data. (see Notes)
<sequence file 2> The name of a sequence file containing input data. (see Notes)
<output file> A plain text file to which the results will be written.

Options that do not require added values:

-l, -L, --logprobability    Print probability matrix as base 10 log probabilities.
-m, -M, --maxlikelihood    Print a maximum likelihood alignment.
-h, -H, --help Display the usage details message.

Output Format:

The default output is a matrix of pair probabilities. Using the -l, -L, --logprobability option changes this to the logarithm, base 10, of the pair probabilities. The matrix is a tab-delimited, plain text file where rows are indices for sequence 1 and columns are indices for sequence 2.

The -m, -M, --maxlikelihood option changes the output a plain text alignment of the two sequences.


  • Unknown nucleotides (e.g. N or X) get randomly mapped to A, C, G, or U by HMM.


  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. Harmanci, A.O., Sharma, G. and Mathews, D.H.
    "Efficient Pairwise RNA Structure Prediction Using Probabilistic Alignment Constraints in Dynalign."
    BMC Bioinformatics, 8:130. (2007).