Man pages for coil
Contextualization and Evaluation of COI-5P Barcode Data
| 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. |
| indel_check | Check if a coi5p sequence likely contains an error. |
| individual_AAbin | build an AAbin with ape. |
| individual_DNAbin | build an DNAbin with ape. |
| ins_front_trim | Check sequence for an early large string of deletions. If it... |
| leading_ins | Check for a large number of leading inserted bases. |
| new_coi5p | Build a new coi5p class instance. |
| nt_coi_PHMM | Nucleotide profile hidden Markov model for coi5p. |
| print.coi5p | Print a summary of a coi5p object. |
| set_frame | Take an input sequence and get it into the reading frame. |
| subsetPHMM | Subset an existing PHMM. |
| trans_df | Data frame containing the translation table recommendation. |
| translate | Translate a coi5p sequence. |
| translate_codon | Censored Translation of a codon. |
| validate_coi5p | Validate the new coi5p class instance. |
| which_trans_table | Determine the translation table to use for a given taxonomic... |
