R: Visually Assessing the Specificity and Informativeness of Primer Pairs

# Visually Assessing the Specificity and Informativeness of Primer Pairs

## Documentation for package ‘primerTree’ version 1.1.0

- DESCRIPTION file

## Help Pages

primerTree-package | 'primerTree' Visually Assessing the Specificity and Informativeness of Primer Pairs
accession2taxid | Maps a nucleotide database accession to a taxonomy database taxId
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.
filter_seqs.primerTree | 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.
get_sequences | Retrieves fasta sequences from NCBI nucleotide database.
get_taxonomy | Retrieve the taxonomy information from NCBI for a set of nucleotide gis.
identify.primerTree_plot | identify the point closest to the mouse click only works on single ranks
layout_tree_ape | layout a tree using ape, return an object to be plotted by 'plot_tree'
mammals_16S | PrimerTree results for the mammalian 16S primers
parse_primer_hits | Parse the primer hits
plot.primerTree | plot function for a primerTree object, calls plot_tree_ranks
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
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 search Search a given primer pair, retrieving the alignment results, their product sequences, taxonomic information for the sequences, a multiple alignment of the products
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 length and pairwise differences.
tree_from_alignment | Construct a neighbor joining tree from a dna alignment