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

[ bioinformatics, gpl, program ] [ Propose Tags ]

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.

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Versions [RSS] 1.0.0, 1.0.1
Dependencies aeson, base (>=4.5 && <5), bytestring, cassava (>=0.4.5.1), cmdargs, directory, either-unwrap, EntrezHTTP (>=1.0.2), fgl, hxt, parsec, process, Taxonomy (>=1.0.2), text, vector [details]
License GPL-3.0-only
Author Florian Eggenhofer
Maintainer egg@tbi.univie.ac.at
Category Bioinformatics
Source repo head: git clone https://github.com/eggzilla/TaxonomyTools
this: git clone https://github.com/eggzilla/TaxonomyTools/tree/1.0.1(tag 1.0.1)
Uploaded by FlorianEggenhofer at 2017-01-26T09:41:48Z
Distributions NixOS:1.0.1
Executables TaxIdsDistance, TaxIds2Tree, TaxIds2TreeCompare, Accessions2TaxIds, TaxIds2Text
Downloads 1646 total (13 in the last 30 days)
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Status Docs not available [build log]
Last success reported on 2017-01-26 [all 3 reports]