| insect-package | Informatic sequence classification trees. | 
| aa2char | Convert sequences between binary and character string formats. | 
| allocateCVI | Allocate sequences for cross validation by identity. | 
| char2aa | Convert sequences between binary and character string formats. | 
| char2dna | Convert sequences between binary and character string formats. | 
| classify | Tree-based sequence classification. | 
| conversion | Convert sequences between binary and character string formats. | 
| decodePHMM | Encode and decode profile HMMs in raw byte format. | 
| demultiplex | Demultiplex merged FASTQ | 
| dereplicate | Dereplicate and rereplicate sequence datasets. | 
| disambiguate | Convert oligonucleotide sequences into regular expressions. | 
| dna2char | Convert sequences between binary and character string formats. | 
| duplicated.AAbin | Further bit-level manipulation of DNA and amino acid sequences. | 
| duplicated.DNAbin | Further bit-level manipulation of DNA and amino acid sequences. | 
| encodePHMM | Encode and decode profile HMMs in raw byte format. | 
| encoding | Encode and decode profile HMMs in raw byte format. | 
| expand | Expand an existing classification tree. | 
| get_lineage | Get full lineage details from a taxonomic ID number. | 
| get_taxID | Get taxon ID from taxonomy database. | 
| hash | Convert sequences to MD5 hashes. | 
| insect | Informatic sequence classification trees. | 
| join | Concatenate DNAbin objects while preserving attributes. | 
| learn | Informatic sequence classification tree learning. | 
| manipulate | Further bit-level manipulation of DNA and amino acid sequences. | 
| prune_taxonomy | Prune taxonomy database. | 
| purge | Identify and remove erroneous reference sequences. | 
| qfilter | Quality filtering for amplicon sequences. | 
| rc | Reverse complement DNA in character string format. | 
| read | Read FASTA and FASTQ files. | 
| readFASTA | Read FASTA and FASTQ files. | 
| readFASTQ | Read FASTA and FASTQ files. | 
| replicate | Dereplicate and rereplicate sequence datasets. | 
| rereplicate | Dereplicate and rereplicate sequence datasets. | 
| samoa | Table of marine COI amplicon sequence variants from American Samoa | 
| searchGB | Query the NCBI GenBank database. | 
| shave | Shave ends from DNA and amino acid sequences | 
| stitch | Paired-end read stitching. | 
| subset.AAbin | Further bit-level manipulation of DNA and amino acid sequences. | 
| subset.DNAbin | Further bit-level manipulation of DNA and amino acid sequences. | 
| taxonomy | Download taxonomy database. | 
| trim | Trim primer and/or index sequences. | 
| unique.AAbin | Further bit-level manipulation of DNA and amino acid sequences. | 
| unique.DNAbin | Further bit-level manipulation of DNA and amino acid sequences. | 
| virtualFISH | Virtual _in situ_ hybridization. | 
| virtualPCR | Virtual PCR. | 
| whales | Cetacean 16S rDNA sequences. | 
| whale_taxonomy | Cetacean section of NCBI taxonomy database. | 
| write | Write sequences to text in FASTA or FASTQ format. | 
| writeFASTA | Write sequences to text in FASTA or FASTQ format. | 
| writeFASTQ | Write sequences to text in FASTA or FASTQ format. |