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Monthly Downloads: 16
Programming language: Haskell
License: GNU General Public License v3.0 only
Latest version: v1.1.0

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README

TaxonomyTools

GitHub Build Status Hackage Bioconda Docker Repository on Quay

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.