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Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export, tree-based sequence weighting, simulation, and implementation of the forward, backward and Viterbi algorithms for calculating sequence probabilities. Standard HMMs are a...

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export, tree-based sequence weighting, simulation, and implementation of the forward, backward and Viterbi algorithms for calculating sequence probabilities. Standard HMMs are a...