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

Current Version

  • TaxonKit v0.5.0 Github Releases (by Release)
    • taxonkit: requiring delnodes.dmp and merged.dmp.
    • taxonkit lineage: detect deleted and merged taxids now. #19
    • taxonkit list/name2taxid: add short flag -r for --show-rank, -n for --show-name.

Links:

Tips

  • run taxonkit version to check update !!!
  • run taxonkit genautocomplete to update Bash completion !!!
OS Arch File, 中国镜像 Download Count
Linux 32-bit taxonkit_linux_386.tar.gz,
中国镜像
Github Releases (by Asset)
Linux 64-bit taxonkit_linux_amd64.tar.gz,
中国镜像
Github Releases (by Asset)
OS X 32-bit taxonkit_darwin_386.tar.gz,
中国镜像
Github Releases (by Asset)
OS X 64-bit taxonkit_darwin_amd64.tar.gz,
中国镜像
Github Releases (by Asset)
Windows 32-bit taxonkit_windows_386.exe.tar.gz,
中国镜像
Github Releases (by Asset)
Windows 64-bit taxonkit_windows_amd64.exe.tar.gz,
中国镜像
Github Releases (by Asset)

Installation

Download Page

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 (latest stable/dev version)

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 copy to anywhere in the environment variable PATH:

      mkdir -p $HOME/bin/; cp taxonkit $HOME/bin/
      
  2. For windows, just copy taxonkit.exe to C:\WINDOWS\system32.

Method 2: Install via conda (latest stable version) Install-with-conda Anaconda Cloud downloads

conda install -c bioconda taxonkit

Method 3: Install via homebrew (latest stable version)

brew install brewsci/bio/taxonkit

Method 4: For Go developer (latest stable/dev version)

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

Bash-completion

Note: The current version supports Bash only. This should work for *nix systems with Bash installed.

Howto:

  1. run: taxonkit genautocomplete

  2. create and edit ~/.bash_completion file if you don't have it.

    nano ~/.bash_completion
    

    add the following:

    for bcfile in ~/.bash_completion.d/* ; do
      . $bcfile
    done
    

Previous Versions

  • TaxonKit v0.4.3 Github Releases (by Release)
    • taxonkit taxid-changelog: rewrite logic, fix bug and add more change types
  • TaxonKit v0.4.2 Github Releases (by Release)
    • taxonkit taxid-changelog: change output of ABSORB, do not merged into one record for changes in different versions.
  • TaxonKit v0.4.1 Github Releases (by Release)
    • taxonkit taxid-changelog:
      • add fields: name and rank.
      • and fix sorting bug.
      • detailed lineage change status
  • TaxonKit v0.4.0 Github Releases (by Release)
    • new command: taxonkit taxid-changelog: for creating taxid changelog from dump archive
  • TaxonKit v0.3.0 Github Releases (by Release)
    • this version is almost the same as v0.2.5
  • TaxonKit v0.2.5 Github Releases (by Release)
    • add global flag: --line-buffered to disable output buffer. #11
    • replace global flags --names-file and --nodes-file with --data-dir, also support environment variable TAXONKIT_DB. #17
    • taxonkit reformat: detects lineages containing unofficial taxon name and won't show panic message.
    • taxonkit name2taxid: supports synonyms names. #9
    • taxokit lineage: add flag -r/--show-rank to print rank at another new column.
  • TaxonKit v0.2.4 Github Releases (by Release)
    • taxonkit reformat:
      • more accurate result when using flag -F/--fill-miss-rank to estimate and fill missing rank with original lineage information
      • supporting escape strings like \t, \n, #5
      • outputting corresponding taxids for reformated lineage. #8
    • taxonkit lineage:
      • fix bug for taxid 1 #7
      • add flag -d/--delimiter.
  • TaxonKit v0.2.3 Github Releases (by Release)
    • fix bug brought in v0.2.1
  • TaxonKit v0.2.2 Github Releases (by Release)
    • make verbose information optional #4
  • TaxonKit v0.2.1 Github Releases (by Release)
    • taxonkit list: fix bug of no output for leaf nodes of the taxonomic tree. #4
    • add new command genautocomplete to generate shell autocompletion script!
  • TaxonKit v0.2.0 Github Releases (by Release)
    • add command name2taxid to query taxid by taxon scientific name.
    • lineage, reformat: changed flags and default operations, check the usage.
  • TaxonKit v0.1.8 Github Releases (by Release)
    • taxonkit lineage, add an extra column of lineage in Taxid. #3. e.g.,
    • fix colorful output in windows.
  • TaxonKit v0.1.7 Github Releases (by Release)
    • taxonkit reformat: supports reading stdin from output of taxonkit lineage, reformated lineages are appended to input data.
  • TaxonKit v0.1.6 Github Releases (by Release)
    • remove flag -f/--formated-rank from taxonkit lineage, using taxonkit reformat can archieve same result.
  • TaxonKit v0.1.5 Github Releases (by Release)
    • reorganize code and flags
  • TaxonKit v0.1.4 Github Releases (by Release)
    • add flag --fill for taxonkit reformat, which estimates and fills missing rank with original lineage information
  • TaxonKit v0.1.3 Github Releases (by Release)
    • add command of taxonkit reformat which reformats full lineage to custom format
  • TaxonKit v0.1.2 Github Releases (by Release)
    • add command of taxonkit lineage, users can query lineage of given taxon IDs from file
  • TaxonKit v0.1.1 Github Releases (by Release)
    • add feature of taxonkit list, users can choose output in readable JSON format by flag --json so the taxonomy tree could be collapse and uncollapse in modern text editor.
  • TaxonKit v0.1 Github Releases (by Release)
    • first release