RNAstructure Command Line Help |
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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:
Options that do not require added values:
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:
References
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