coil: Contextualization and Evaluation of COI-5P Barcode Data

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.

Version:	1.2.4
Depends:	R (≥ 3.0.0)
Imports:	ape, aphid, seqinr
Suggests:	knitr, rmarkdown, testthat
Published:	2024-01-11
DOI:	10.32614/CRAN.package.coil
Author:	Cameron M. Nugent
Maintainer:	Cameron M. Nugent <camnugent at gmail.com>
License:	GPL-3
NeedsCompilation:	no
Materials:	README
CRAN checks:	coil results

Documentation:

Reference manual:	coil.pdf
Vignettes:	Introduction to the coil package

Downloads:

Package source:	coil_1.2.4.tar.gz
Windows binaries:	r-devel: coil_1.2.4.zip, r-release: coil_1.2.4.zip, r-oldrel: coil_1.2.4.zip
macOS binaries:	r-release (arm64): coil_1.2.4.tgz, r-oldrel (arm64): coil_1.2.4.tgz, r-release (x86_64): coil_1.2.4.tgz, r-oldrel (x86_64): coil_1.2.4.tgz
Old sources:	coil archive

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