Taxonomy: Libary for parsing, processing and vizualization of taxonomy data

[ bioinformatics, gpl, library ] [ Propose Tags ]

Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation for the NCBI (National Center for Biotechnology Information) Taxonomy datasources.

It can utilize information from the Entrez REST interface via EntrezHTTP, as well as from the files of the Taxonomy database dump.

Input data is parsed into a FGL based datastructure, which enables a wealth of processing steps like node distances, retrieval of parent nodes or extraction of subtrees.

Trees can be visualised via dot-format (graphviz)

or via json-format (http://d3js.org/d3js).

The TaxonomyTools package contains tools based on this package.


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Versions [faq] 1.0.1, 1.0.2, 1.0.3, 2.0.0, 2.1.0
Change log ChangeLog.md
Dependencies aeson, base (>=4.5 && <5), bytestring, either-unwrap, fgl (>=5.5.4.0), parsec, text, vector [details]
License GPL-3.0-only
Author Florian Eggenhofer
Maintainer egg@informatik.uni-freiburg.de
Category Bioinformatics
Source repo head: git clone https://github.com/eggzilla/Taxonomy
this: git clone https://github.com/eggzilla/Taxonomy/tree/v2.1.0(tag v2.1.0)
Uploaded by FlorianEggenhofer at 2019-12-17T15:27:55Z
Distributions NixOS:2.1.0
Downloads 3013 total (12 in the last 30 days)
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Status Hackage Matrix CI
Docs available [build log]
Last success reported on 2019-12-17 [all 1 reports]

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Readme for Taxonomy-2.1.0

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Taxonomy Hackage Build Status

Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation for the NCBI (National Center for Biotechnology Information) Taxonomy datasources.

It can utilize information from the Entrez REST interface (via EntrezHTTP, as well as from the files of the Taxonomy database dump.

Input data is parsed into a FGL based datastructure, which enables a wealth of processing steps like node distances, retrieval of parent nodes or extraction of subtrees.

Trees can be visualised via dot-format (graphviz) or via json-format (d3js).