Informatic Sequence Classification Trees

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Documentation for package ‘insect’ version 1.4.2

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

Help Pages

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.