primerTree v1.0.4


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Visually Assessing the Specificity and Informativeness of Primer Pairs

Identifies potential target sequences for a given set of primers and generates phylogenetic trees annotated with the taxonomies of the predicted amplification products.

Functions in primerTree

Name Description
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
tree_from_alignment Construct a neighbor joining tree from a dna alignment
get_taxonomy Retrieve the taxonomy information from NCBI for a set of nucleotide gis.
layout_tree_ape layout a tree using ape, return an object to be plotted by plot_tree
seq_lengths.primerTree Method for primerTree objects
mammals_16S PrimerTree results for the mammalian 16S primers
summary.primerTree Summarize a primerTree result, printing quantiles of sequence length and pairwise differences.
plot.primerTree plot function for a primerTree object, calls plot_tree_ranks
parse_primer_hits Parse the primer hits
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
get_sequences Retrieves fasta sequences from NCBI nucleotide database.
accession2gi Maps a genbank accession to a nuclotide database gi.
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 single ranks
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.
get_sequence Retrieves a fasta sequence from NCBI nucleotide database.
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LazyData true
License GPL-2
Packaged 2018-12-19 18:29:43 UTC; jhester
RoxygenNote 6.0.1
NeedsCompilation yes
Repository CRAN
Date/Publication 2018-12-19 18:50:03 UTC

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