ncbitax- a simple NCBI taxonomy parser
A very light-weight straight-forward parser for NCBI taxonomy, for simple lineage retrieval, and common ancestor searches.
git clone [email protected]: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.
scripts/setup.sh to an Rmarkdown vignette for the
R package, and move shell, Perl and R scripts to R package location
getID: catch missing and resolve multiple hits
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