debar

debar is an R package designed for denoising sequence data for the animal DNA barcode marker: cytochrome c oxidase I (COI-5P, or the five prime portion of COI). The package is designed to detect and correct insertion and deletion errors within barcode sequences. This is accomplished through comparison of input sequences against a profile hidden Markov (PHMM) model using the Viterbi algorithm and adjustment of the sequence based on the reported Viterbi path (debar depends on functions from the R package aphid for the PHMM structure and for running the Viterbi algorithm).