accession2taxid         Maps a nucleotide database accession to a
                        taxonomy database taxId
bryophytes_trnL         PrimerTree results for the bryophyte trnL
                        primers
calc_rank_dist_ave      Summarize pairwise differences.
clustalo                Multiple sequence alignment with clustal omega
filter_seqs             Filter out sequences retrieved by
                        search_primer_pair() that are either too short
                        or too long. The alignment and tree will be
                        recalculated after removing unwanted reads.
get_sequence            Retrieves a fasta sequence from NCBI nucleotide
                        database.
get_sequences           Retrieves fasta sequences from NCBI nucleotide
                        database.
get_taxonomy            Retrieve the taxonomy information from NCBI for
                        a set of nucleotide gis.
identify.primerTree_plot
                        identify the point closest to the mouse click
                        only works on single ranks
layout_tree_ape         layout a tree using ape, return an object to be
                        plotted by 'plot_tree'
mammals_16S             PrimerTree results for the mammalian 16S
                        primers
parse_primer_hits       Parse the primer hits
plot.primerTree         plot function for a primerTree object, calls
                        plot_tree_ranks
plot_tree               plots a tree, optionally with colored and
                        labeled points by taxonomic rank
plot_tree_ranks         plots a tree along with a series of taxonomic
                        ranks
primerTree              'primerTree' Visually Assessing the Specificity
                        and Informativeness of Primer Pairs
primer_search           Query a pair of primers using ncbi's
                        Primer-BLAST, if primers contain iupac
search_primer_pair      Automatic primer search Search a given primer
                        pair, retrieving the alignment results, their
                        product sequences, taxonomic information for
                        the sequences, a multiple alignment of the
                        products
seq_lengths             Get a summary of sequence lengths from a
                        primerTree object
seq_lengths.primerTree
                        Method for primerTree objects
summary.primerTree      Summarize a primerTree result, printing
                        quantiles of sequence length and pairwise
                        differences.
tree_from_alignment     Construct a neighbor joining tree from a dna
                        alignment
