aa_PHMM

<p>This model is stored in the coi5p package and was trained on a representative
sample of the barcode of life database (http://www.boldsystems.org/index.php).</p>

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Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI).
It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing
the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences
against nucleotide and amino acid profile hidden Markov models (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically
diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted
analysis of barcode data.

Cameron Nugent

coil

Contextualization and Evaluation of COI-5P Barcode Data

aa_PHMM function

<p>An object of class <code>PHMM</code> of length 14.</p>

aa_PHMM: Amino acid profile hidden Markov model for coi5p.

Description

Usage

Arguments

Format