Visually Assessing the Specificity and Informativeness of Primer Pairs

[Up] [Top]

Documentation for package ‘primerTree’ version 1.0.6

Help Pages

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 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
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