Contextualization and Evaluation of COI-5P Barcode Data

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Documentation for package ‘coil’ version 1.2.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

aa_coi_PHMM	Amino acid profile hidden Markov model for coi5p.
censored_translation	Censored Translation of a DNA string.
coi5p	Build a coi5p object from a DNA sequence string.
coi5p_pipe	Run the entire coi5p pipeline for an input sequence.
coil	'coil': evaluation of COI-5P barcode data
example_barcode_data	Example barcode data.
example_nt_string	Example coi5p DNA sequence string
flatten_coi5p	Flatten a list of coi5p output objects into a dataframe.
frame	Take a coi5p sequence and place it in reading frame.
frame.coi5p	Take a coi5p sequence and place it in reading frame.
indel_check	Check if a coi5p sequence likely contains an error.
indel_check.coi5p	Check if a coi5p sequence likely contains an error.
nt_coi_PHMM	Nucleotide profile hidden Markov model for coi5p.
subsetPHMM	Subset an existing PHMM.
translate	Translate a coi5p sequence.
translate.coi5p	Translate a coi5p sequence.
trans_df	Data frame containing the translation table recommendation.
which_trans_table	Determine the translation table to use for a given taxonomic group.