R: Informatic Sequence Classification Trees

# Informatic Sequence Classification Trees

## Documentation for package ‘insect’ version 1.4.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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.