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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 (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 |
| Reference manual: | coil.pdf |
| Vignettes: |
Introduction to the coil package |
| 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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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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