https://github.com/eggzilla/taxonomytools

Tools to process and visualize NCBI taxonomy data
https://github.com/eggzilla/taxonomytools

bioinformatics taxonomy

Last synced: 13 days ago
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Tools to process and visualize NCBI taxonomy data

• Host: GitHub
• URL: https://github.com/eggzilla/taxonomytools
• Owner: eggzilla
• License: gpl-3.0
• Created: 2015-05-29T16:55:36.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2021-05-31T19:18:11.000Z (over 3 years ago)
• Last Synced: 2024-11-03T11:42:46.871Z (2 months ago)
• Topics: bioinformatics, taxonomy
• Language: Haskell
• Homepage:
• Size: 74.2 KB
• Stars: 3
• Watchers: 5
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: ChangeLog.md
  • License: LICENSE

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README

        
![TaxonomyTools](http://www.tbi.univie.ac.at/~egg/TaxonomyTools.png "TaxonomyTools")

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=============

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.

TaxonomyTools can be install via the Haskell package management system:

    cabal install TaxonomyTools

Currently following Tools are included and linked with their usage instructions:

###[Accessions2TaxIds](accessions2taxids.md)

Converts a list of Refseq accession numbers into NCBI taxonomy ids

###[TaxIds2Tree](taxids2tree.md)

List of taxonomy ids is converted into a graphical tree representation

either as .svg (via graphviz) or as .json (via d3js)

###[TaxIds2TreeCompare](taxids2treecompare.md)

Multiple lists of taxonomy ids are converted into a visualisation of the

taxonomic tree highlighting the input nodes corresponding to their list. 

###[TaxIds2Text](taxids2text.md)

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

###[TreeDistance](taxis2distance.md)

Computes the distance between two input nodes on the given tree.