primerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs

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

Install the latest version of this package by entering the following in R:
install.packages("primerTree")
AuthorJim Hester
Date of publication2016-01-12 22:04:30
MaintainerJim Hester <james.f.hester@gmail.com>
LicenseGPL-2
Version1.0.3

View on CRAN

Man pages

accession2gi: Maps a genbank accession to a nuclotide database gi.

bryophytes_trnL: PrimerTree results for the bryophyte trnL primers

clustalo: Multiple sequence alignment with clustal omega

filter_seqs: Filter out sequences retrieved by search_primer_pair() that...

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...

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...

layout_tree_ape: layout a tree using ape, return an object to be plotted by...

mammals_16S: PrimerTree results for the mammalian 16S primers

plot.primerTree: plot function for a primerTree object, calls plot_tree_ranks

plot_tree: plots a tree, optionally with colored and labeled points by...

plot_tree_ranks: plots a tree along with a series of taxonomic ranks

primer_search: Query a pair of primers using ncbi's Primer-BLAST, if primers...

primerTree: 'primerTree' Visually Assessing the Specificity and...

search_primer_pair: Automatic primer searching Search a given primer pair,...

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...

tree_from_alignment: Construct a neighbor joining tree from a dna alignment

Functions

accession2gi Man page
bryophytes_trnL Man page
clustalo Man page
filter_seqs Man page
filter_seqs.primerTree Man page
get_sequence Man page
get_sequences Man page
get_taxonomy Man page
gi2taxid Man page
identify.primerTree_plot Man page
layout_tree_ape Man page
mammals_16S Man page
plot.primerTree Man page
plot_tree Man page
plot_tree_ranks Man page
primer_search Man page
primerTree Man page
primerTree-package Man page
search_primer_pair Man page
seq_lengths Man page
seq_lengths.primerTree Man page
summary.primerTree Man page
tree_from_alignment Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.