taxonkit

README

TaxonKit - Cross-platform and Efficient NCBI Taxonomy Toolkit

• Documents: http://bioinf.shenwei.me/taxonkit (Usage, Tutorial)
• Source code: https://github.com/shenwei356/taxonkit
• Latest version:

Subcommands

• list list taxon tree of given taxids
• lineage query lineage of given taxids from file/stdin
• reformat reformat lineage

Installation

Go to Download Page for more download options and changelogs.

TaxonKit is implemented in Go programming language, executable binary files for most popular operating systems are freely available in release page.

Method 1: Download binaries

Just download compressed executable file of your operating system, and decompress it with tar -zxvf *.tar.gz command or other tools. And then:

1. For Linux-like systems

   1. If you have root privilege simply copy it to /usr/local/bin:

       sudo cp taxonkit /usr/local/bin/
      

   2. Or add the current directory of the executable file to environment variable PATH:

       echo export PATH=\$PATH:\"$(pwd)\" >> ~/.bashrc
       source ~/.bashrc
      

2. For windows, just copy taxonkit.exe to C:\WINDOWS\system32.

Method 2: Install via conda

conda install -c bioconda taxonkit

Method 3: For Go developer

go get -u github.com/shenwei356/taxonkit/taxonkit

Contact

Email me for any problem when using taxonkit. shenwei356(at)gmail.com

Create an issue to report bugs, propose new functions or ask for help.

License

MIT License