which_trans_table

Recommends which translation table to use if taxonomic data are available.
The recommendations are based on the translation tables reported for different
taxonomic classifications on the Barcode of Life Data Systems
(BOLD - http://www.boldsystems.org/index.php).

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

which_trans_table function

<dl><dt>x</dt>
<dd>A taxonomic designation (allowed ranks: family, order, class, phylum).</dd></dl>

Arguments

Determine the translation table to use for a given taxonomic group. — which_trans_table

<dl>

<dt>x</dt>
<dd>A taxonomic designation (allowed ranks: family, order, class, phylum).</dd>

</dl>

which_trans_table: Determine the translation table to use for a given taxonomic group.

Description

Usage

Value

Arguments

Details

Examples