primerTree (version 1.1.0)

Visually Assessing the Specificity and Informativeness of Primer Pairs

Description

Identifies potential target sequences for a given set of primers and generates phylogenetic trees annotated with the taxonomies of the predicted amplification products.

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Version

Install

install.packages('primerTree')

Monthly Downloads

346

Version

1.1.0

License

GPL-2

Maintainer

Matt Cannon

Last Published

October 3rd, 2025

Functions in primerTree (1.1.0)

get_taxonomy

Retrieve the taxonomy information from NCBI for a set of nucleotide gis.

seq_lengths

Get a summary of sequence lengths from a primerTree object

seq_lengths.primerTree

Method for primerTree objects

bryophytes_trnL

PrimerTree results for the bryophyte trnL primers

accession2taxid

Maps a nucleotide database accession to a taxonomy database taxId

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.

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

mammals_16S

PrimerTree results for the mammalian 16S primers

parse_primer_hits

Parse the primer hits

get_sequence

Retrieves a fasta sequence from NCBI nucleotide database.

calc_rank_dist_ave

Summarize pairwise differences.

clustalo

Multiple sequence alignment with clustal omega

plot_tree_ranks

plots a tree along with a series of taxonomic ranks

primerTree

primerTree Visually Assessing the Specificity and Informativeness of Primer Pairs

plot_tree

plots a tree, optionally with colored and labeled points by taxonomic rank

plot.primerTree

plot function for a primerTree object, calls plot_tree_ranks

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

identify.primerTree_plot

identify the point closest to the mouse click only works on single ranks

get_sequences

Retrieves fasta sequences from NCBI nucleotide database.

layout_tree_ape

layout a tree using ape, return an object to be plotted by plot_tree