TaxonomyTools: Tool for parsing, processing, comparing and visualizing taxonomy data

Taxonomy Tool utilizes functions from the Taxonomy library to provide

several commandline utilities for routine-tasks with taxonomy data.

Currently some tools accept either the NCBI taxonomy dump as input,

while other retrieve the data directly from the NCBI Entrez REST interface.

It is planned to support both datasources with each tool.

Usage instructions can be found in the README

Currently following Tools are included:

• Accessions2TaxIds: Converts a list of NCBI accession numbers into NCBI taxonomy ids

• TaxIds2Tree: List of taxonomy ids is converted into a graphical tree representation either as .svg (via graphviz) or as .json (via d3js).

• TaxIds2TreeCompare: Multiple lists of taxonomy ids are converted into a visualisation of the taxonomic tree highlighting the input nodes corresponding to their list.

• TaxIds2Text: List of taxonomy ids is converted in a short text summary for each node.

• TreeDistance: Computes the distance between two input nodes on the given tree.

Downloads

• TaxonomyTools-1.0.1.tar.gz [browse] (Cabal source package)
• Package description (as included in the package)

Maintainer's Corner

Package maintainers

• FlorianEggenhofer

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