Contextualization and Evaluation of COI-5P Barcode Data


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Documentation for package ‘coil’ version 1.2.3

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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.