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src/Bio
.travis.yml
LICENSE
README.md
Setup.hs
TaxonomyTools.cabal
TaxonomyTools.svg
accessions2taxids.md
changelog
taxids2text.md
taxids2tree.md
taxids2treecompare.md
taxidsdistance.md

README.md

TaxonomyTools

Hackage Build Status

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 Converts a list of Refseq 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.