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primerTree (version 1.0.4)

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

199

Version

1.0.4

License

GPL-2

Maintainer

Jim Hester

Last Published

December 19th, 2018

Functions in primerTree (1.0.4)

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
tree_from_alignment

Construct a neighbor joining tree from a dna alignment
get_taxonomy

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

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

Method for primerTree objects
mammals_16S

PrimerTree results for the mammalian 16S primers
summary.primerTree

Summarize a primerTree result, printing quantiles of sequence length and pairwise differences.
plot.primerTree

plot function for a primerTree object, calls plot_tree_ranks
parse_primer_hits

Parse the primer hits
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 searching Search a given primer pair, retrieving the alignment results, their product sequences, the taxonomic information for the sequences, a multiple alignment of the products
seq_lengths

Get a summary of sequence lengths from a primerTree object
get_sequences

Retrieves fasta sequences from NCBI nucleotide database.
accession2gi

Maps a genbank accession to a nuclotide database gi.
gi2taxid

Maps a nucleotide database gi to a taxonomy database taxId
identify.primerTree_plot

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