Function reference • taxreturn

All functions
`DNAbin2DNAstringset()`	Convert DNABin to DNAStringSet
`DNAbin2char()`	DNAbin to char
`acc2hex()`	Convert accession number to hexadecimal coding
`acc_from_fasta()`	Genbank accessions from fasta
`alignment_entropy()`	Alignment entropy
`blast()`	Run BLAST search
`blast_assign_species()`	Assign species using BLAST
`blast_install()`	Install BLAST
`blast_params()`	Show BLAST parameters
`blast_top_hit()`	BLAST Top Hit
`char2DNAbin()`	char2DNAbin
`clean_seqs()`	Clean Sequences with PHMM (DEPRECATED)
`closest_seq()`	Closest kmer distance This function checks the kmer distance between all the sequences in a DNAbin and a reference PHMM model
`codon_entropy()`	Codon entropy
`codon_filter()`	Filter sequences containing stop codons
`concat_DNAbin()`	Concatenate DNAbin objects while preserving attributes. This function joins two or more `DNAbin` objects, retaining any attributes whose lengths match those of the input objects (e.g. "species", "lineage" and/or "taxID" attributes).
`.findExecutable()`	Find executable
`.hex()`	convert alphanumerics to hexadecimal internal taxreturn function
`.ishex()`	Check whether a string is hexadecimal internal taxreturn function
`.unhex()`	convert hexadecimal strings to alphanumeric internal taxreturn function
`download_ott_taxonomy()`	Download open tree of life taxonomy
`fetchSeqs()`	Fetchseqs function (DEPRECATED)
`fetch_bold()`	Fetch sequences from BOLD
`fetch_genbank()`	all `[filter]` Retrieves everthing Specified `[property]` Formal binomial and trinomial at or below species level `[property]` family `[rank]` Rank-based query taxonomy genome `[filter]` Taxa with a direct link to a genome sequence 2009/10/21:2020 `[date]` Date-bounded query mammalia `[subtree]` All taxa within the Mammalia extinct `[property]` Extinct organisms Terminal `[property]` Terminal nodes in the tree loprovencyclife `[filter]` Entries with LinkOut links to the Encyclopedia of Life
`fetch_seqs()`	fetch_seqs function
`filter_by_tax()`	Filter sequences by taxonomy
`filter_infraspecifc()`	Filter infraspecific taxonomic labels
`filter_unplaced()`	Filter unplaced taxonomic labels
`get_binding_position()`	Get primer binding position
`get_mixed_clusters()`	Get mixed clusters
`get_ncbi_lineage()`	Get lineage
`get_ncbi_synonyms()`	Get NCBI synonyms
`get_ncbi_taxonomy()`	Download NCBI taxdump
`get_ott_lineage()`	Recursively get lineage from OTT taxid This function derives the full lineage of a taxon ID number from a given taxonomy database
`get_ott_taxonomy()`	get_ott_taxonomy
`get_reading_frame()`	Get Reading frame of sequences
`get_subalignment()`	Get subalignment
`gid_to_acc()`	Convert NCBI gene ids to accession numbers
`graft_tips()`	Graft new tips onto an existing tree
`hex2acc()`	Hexadecimal coding to accession numberD
`kmer_screen()`	Kmer screening function
`lca_probs()`	Probabilitys of sharing a rank as a function of sequence identity
`make_blast_db()`	Make blast Database
`makeblastdb()`	Make blast Database (DEPRECATED)
`map_to_model()`	Map to model
`map_to_ott()`	Map taxa to open tree of life
`model`	COI phmm model
`ncbi_taxid()`	Get ncbi taxid's for a taxon name
`pad_alignment()`	Pad alignment
`parse_gb()`	Parse genbank flat files
`parse_ott_synonyms()`	parse the open tree of life synonyms file
`propagate_tax()`	Propagate taxonomy (DEPRECATED)
`prune_groups()`	Prune group sizes
`random_seq()`	Generate random sequences
`read_bold_chunk()`	read bold chunk
`read_genbank_chunk()`	Read genbank chunk
`reformat_dada2_gen()`	Reformat DADA2 Genus
`reformat_dada2_spp()`	Reformat DADA2 Species
`reformat_hierarchy()`	Reformat hierarchy
`resolve_synonyms_ncbi()`	resolve_synonyms_ncbi
`setup_multithread()`	Setup multithreading
`setup_para()`	Setup parallel
`split_bold_query()`	Split bold query This function recursively splits a bold taxonomic query until the amount of records returned is under chunk_size
`subset_model()`	Subset PHMM Modified from Cameron Nugent's COIL package https://github.com/CNuge/coil/blob/master/R/subset_PHMM.r
`summarise_fasta()`	summarise_fasta
`tax2phylo()`	tax2phylo
`tax2tree()`	tax2tree
`train_idtaxa()`	Train IDTAXA
`write_fasta()`	write fasta

Reference

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