| ## RNAstructure Command Line Help phmm | ### Contents ### Index
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. ### Notes: Unknown nucleotides (e.g. N or X) get randomly mapped to A, C, G, or U by HMM. ### References Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010). 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).