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.

AuthorJim Hester
Date of publication2016-01-12 22:04:30
MaintainerJim Hester <>

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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

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