nt_coi_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>

datasets

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 (PHMMs) (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

nt_coi_PHMM function

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

nt_coi_PHMM: Nucleotide profile hidden Markov model for coi5p.

Description

Usage

Arguments

Format