Taxonomy

Libary for parsing, processing and vizualization of taxonomy data

LTS Haskell 18.28:	2.2.0
Stackage Nightly 2022-02-07:	2.2.0
Latest on Hackage:	2.2.0

See all snapshots Taxonomy appears in

GPL-3.0-only licensed by Florian Eggenhofer

Maintained by egg@informatik.uni-freiburg.de

This version can be pinned in stack with:Taxonomy-2.2.0@sha256:ed4209c2e8f696920f51531bb84cb1f8e81a4614c48eb00ae7b5e1385e9497ac,2454

Module documentation for 2.2.0

Biobase
- Biobase.Taxonomy

Depends on 9 packages(full list with versions):

aeson, base, bytestring, either-unwrap, fgl, graphviz, parsec, text, vector

Taxonomy

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).

Changes

--change-log-- 2.2.0 Florian Eggenhofer 30. May 2020

    * Compatibility with 9.0.1, reintegrated visualisation libraries

2.1.0 Florian Eggenhofer 17. December 2019

* Moved visualisation code to own library

2.0.0 Florian Eggenhofer 18. November 2019

* Changed to Biobase repository layout
* Added new Lineage datatype
* Using bytestring instead of string

1.0.3 Florian Eggenhofer 10. August 2017

* Compatibility with newest versions of fgl
* Improved travis file

1.0.2 Florian Eggenhofer 23. October 2016

* Changed datastructures for cutting the tree from list to vectors
* Improved travis file