Parse the primer hits
Get a summary of sequence lengths from a primerTree object
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
Summarize a primerTree result, printing quantiles of sequence length and
pairwise differences.
Method for primerTree objects
primerTree Visually Assessing the Specificity and Informativeness of Primer Pairs
Construct a neighbor joining tree from a dna alignment
Query a pair of primers using ncbi's Primer-BLAST, if primers contain iupac
plots a tree, optionally with colored and labeled points by taxonomic rank
plots a tree along with a series of taxonomic ranks
plot function for a primerTree object, calls plot_tree_ranks
PrimerTree results for the mammalian 16S primers
layout a tree using ape, return an object to be plotted by
plot_tree identify the point closest to the mouse click
only works on single ranks
PrimerTree results for the bryophyte trnL primers
Maps a nucleotide database gi to a taxonomy database taxId
Retrieve the taxonomy information from NCBI for a set of nucleotide gis.
Summarize pairwise differences.
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.
Maps a genbank accession to a nuclotide database gi.
Retrieves fasta sequences from NCBI nucleotide database.
Multiple sequence alignment with clustal omega
Retrieves a fasta sequence from NCBI nucleotide database.