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