README.md

ncbitax - a simple NCBI taxonomy parser

A very light-weight straight-forward parser for NCBI taxonomy, for simple lineage retrieval, and common ancestor searches.

Installation, Quick Start & Usage

With devtools from git

library(devtools)
install_github("raim/ncbitax")

Source code from github

git clone [email protected]:raim/ncbitax.git
R CMD build ncbitax
sudo R CMD INSTALL ncbitax_0.0.1.tar.gz

Use of this Package

This package allows to browse the NCBI taxonomy and extract sub-trees via sets of NCBI taxonomy IDs, eg. from a local blast database or genome-scanning results. The results can then be interpreted along the taxonomic tree or alignment-based phylogenetic trees, mapped to NCBI taxonomy IDs.

See the bash script scripts/setup.sh how to download NCBI taxonomy, database, the Silva 16S rRNA tree and a protein consensus tree from cyanobacteria and map all trees to NCBI taxonomy identifiers.

TODO



raim/ncbitax documentation built on Nov. 5, 2019, 2:08 a.m.