TaxonomyTools alternatives and similar packages
Based on the "Bioinformatics" category.
Alternatively, view TaxonomyTools alternatives based on common mentions on social networks and blogs.
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cobot
Computational biology toolkit to collaborate with researchers in constructive protein engineering -
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BlastHTTP
Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice -
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EntrezHTTP
Haskell cabal libary for submission and result retrieval from the NCBI Entrez REST webservice -
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Taxonomy
Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation for the NCBI (National Center for Biotechnology Information) Taxonomy datasources. -
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StockholmAlignment
Libary containing parsing and visualisation functions and datastructures for Stockholm aligmnent format. -
BioHMM
Libary containing parsing and visualisation functions and datastructures for Hidden Markov Models in HMMER3 format. -
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rank-product
Collects the functions pertaining to finding the rank product of a data set as well as the associated p-value. -
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InfluxDB – Built for High-Performance Time Series Workloads
Do you think we are missing an alternative of TaxonomyTools or a related project?
README
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.