ncbitax
- a simple NCBI taxonomy parserA very light-weight straight-forward parser for NCBI taxonomy, for simple lineage retrieval, and common ancestor searches.
devtools
from gitlibrary(devtools)
install_github("raim/ncbitax")
github
git clone git@github.com:raim/ncbitax.git
R CMD build ncbitax
sudo R CMD INSTALL ncbitax_0.0.1.tar.gz
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.
convert scripts/setup.sh
to an Rmarkdown vignette for the
R package, and move shell, Perl and R scripts to R package location
for scripts
generate a small sample taxonomy to allow examples to run
getID: catch missing and resolve multiple hits
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