Man pages for primerTree
Visually Assessing the Specificity and Informativeness of Primer Pairs
| accession2taxid | Maps a nucleotide database accession to a taxonomy database... |
| 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... |
| 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... |
| 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 |
| 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... |
| 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 |
