primerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs

Share:

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

Author
Jim Hester
Date of publication
2016-01-12 22:04:30
Maintainer
Jim Hester <james.f.hester@gmail.com>
License
GPL-2
Version
1.0.3

View on CRAN

Man pages

accession2gi
Maps a genbank accession to a nuclotide database gi.
bryophytes_trnL
PrimerTree results for the bryophyte trnL primers
clustalo
Multiple sequence alignment with clustal omega
filter_seqs
Filter out sequences retrieved by search_primer_pair() that...
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...
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...
layout_tree_ape
layout a tree using ape, return an object to be plotted by...
mammals_16S
PrimerTree results for the mammalian 16S primers
plot.primerTree
plot function for a primerTree object, calls plot_tree_ranks
plot_tree
plots a tree, optionally with colored and labeled points by...
plot_tree_ranks
plots a tree along with a series of taxonomic ranks
primer_search
Query a pair of primers using ncbi's Primer-BLAST, if primers...
primerTree
'primerTree' Visually Assessing the Specificity and...
search_primer_pair
Automatic primer searching Search a given primer pair,...
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...
tree_from_alignment
Construct a neighbor joining tree from a dna alignment

Files in this package

primerTree
primerTree/src
primerTree/src/read_dna.c
primerTree/NAMESPACE
primerTree/data
primerTree/data/mammals_16S.RData
primerTree/data/bryophytes_trnL.RData
primerTree/R
primerTree/R/filterResults.R
primerTree/R/plot.R
primerTree/R/sequence.R
primerTree/R/taxonomy.R
primerTree/R/search.R
primerTree/R/primerTree.R
primerTree/MD5
primerTree/DESCRIPTION
primerTree/man
primerTree/man/filter_seqs.Rd
primerTree/man/get_taxonomy.Rd
primerTree/man/primerTree.Rd
primerTree/man/get_sequence.Rd
primerTree/man/plot_tree.Rd
primerTree/man/search_primer_pair.Rd
primerTree/man/summary.primerTree.Rd
primerTree/man/bryophytes_trnL.Rd
primerTree/man/primer_search.Rd
primerTree/man/plot.primerTree.Rd
primerTree/man/plot_tree_ranks.Rd
primerTree/man/seq_lengths.Rd
primerTree/man/clustalo.Rd
primerTree/man/layout_tree_ape.Rd
primerTree/man/accession2gi.Rd
primerTree/man/identify.primerTree_plot.Rd
primerTree/man/get_sequences.Rd
primerTree/man/gi2taxid.Rd
primerTree/man/mammals_16S.Rd
primerTree/man/seq_lengths.primerTree.Rd
primerTree/man/tree_from_alignment.Rd