DownloadLink

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

Current VersionLink

TaxonKit v0.20.0

This version is mainly for maintaining compatibility with NCBI's recent changes(1, 2).
Please remove the ranks.txt file in ~/.taxonkit/ or other directories containing taxdump files (nodes.dmp).
- taxonkit reformat:
  - Tried to make it compatible with NCBI's recent changes but failed.
  - Update doc to recommend using taxonkit reformat2.
- taxonkit reformat:
  - Fix handling of deleted TaxIds. #117
  - Change the default output format to be compatible with NCBI's recent changes. #115, #116)
- taxonkit filter2:
  - Support new ranks: acellular root and cellular root. Please remove the ranks.txt file in ~/.taxonkit/ or other directories containing taxdump files (nodes.dmp).
  - Automaticlly switch on -N/--discard-noranks when only -E/--equal-to is given and the value is not one of ranks without order ("no rank", "clade").
- taxonkit name2taxid:
  - Remove duplicated records caused by capitalization.

Please citeLink

Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit, Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006

LinksLink

Tips

run taxonkit version to check update !!!
run taxonkit genautocomplete to update Bash completion !!!

OS	Arch	File, 中国镜像
Linux	64-bit	taxonkit_linux_amd64.tar.gz, 中国镜像
Linux	arm64	taxonkit_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	taxonkit_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	taxonkit_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	taxonkit_windows_amd64.exe.tar.gz, 中国镜像

InstallationLink

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)Link

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

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

Method 2: Install via conda (latest stable version) Link

conda install -c bioconda taxonkit

Method 3: Install via homebrew (may not the lastest version)Link

brew install brewsci/bio/taxonkit

Method 4: Compile from source (latest stable/dev version)Link

Install go

wget https://go.dev/dl/go1.24.2.linux-amd64.tar.gz

tar -zxf go1.24.2.linux-amd64.tar.gz -C $HOME/

# or 
#   echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc
#   source ~/.bashrc
export PATH=$PATH:$HOME/go/bin

Compile TaxonKit

git clone https://github.com/shenwei356/taxonkit
cd taxonkit/taxonkit/
go build

# The executable binary file is located in:
#   ./taxonkit
# You can also move it to anywhere in the $PATH
mkdir -p $HOME/bin
cp ./taxonkit $HOME/bin/

Bash-completionLink

Supported shell: bash|zsh|fish|powershell

Bash:

# generate completion shell
taxonkit genautocomplete --shell bash

# configure if never did.
# install bash-completion if the "complete" command is not found.
echo "for bcfile in ~/.bash_completion.d/* ; do source \$bcfile; done" >> ~/.bash_completion
echo "source ~/.bash_completion" >> ~/.bashrc

Zsh:

# generate completion shell
taxonkit genautocomplete --shell zsh --file ~/.zfunc/_taxonkit

# configure if never did
echo 'fpath=( ~/.zfunc "${fpath[@]}" )' >> ~/.zshrc
echo "autoload -U compinit; compinit" >> ~/.zshrc

fish:

taxonkit genautocomplete --shell fish --file ~/.config/fish/completions/taxonkit.fish

DatasetLink

Download and uncompress taxdump.tar.gz: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
Copy names.dmp, nodes.dmp, delnodes.dmp and merged.dmp to data directory: $HOME/.taxonkit, e.g., /home/shenwei/.taxonkit ,
Optionally copy to some other directories, and later you can refer to using flag --data-dir, or environment variable TAXONKIT_DB.

All-in-one command:

wget -c ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
tar -zxvf taxdump.tar.gz

mkdir -p $HOME/.taxonkit
cp names.dmp nodes.dmp delnodes.dmp merged.dmp $HOME/.taxonkit

Update dataset: Simply re-download the taxdump files, uncompress and override old ones.

Release historyLink

TaxonKit v0.19.0
- new command taxonkit reformat2: Reformat lineage in chosen ranks, allowing more ranks than 'reformat'
- taxonkit reformat:
  - Fix -T/--trim which did not work for -r/--miss-rank-repl. #106
TaxonKit v0.18.0
- taxonkit reformat:
  - Add a placeholder for rank "realm", "{r}", which is common in Virus taxonomy like ictv. #102
- taxonkit name2taxid:
  - Show warning for names with multiple taxids. #103
TaxonKit v0.17.0
- taxonkit filter:
  - Fix keeping taxids with a rank of "no rank" or "clade". #97
- taxonkit list:
  - Accept input TaxIds from stdin/files, not just the flag --ids. #93
- taxonkit name2taxid:
  - Add support of fuzzy match with -f/--fuzzy. #88
- taxonkit profile2cami:
  - Add a new flag -S/--no-sum-up to disable summing up abundances. #99
TaxonKit v0.16.0
- taxonkit create-taxdump:
  - TaxIds are generated from the hash value of "rank+taxon_name", this allowed duplicated names with different ranks (common in GTDB). #92.
- taxonkit taxid-changelog/create-taxdump:
  - Add notes about the possible error records in taxid-changelog built from taxonomic data created by create-taxdump. #91
  - Dont't worry, a single version of taxonomic data created by taxonkit create-taxdump has no problem, it's just the changelog might not be perfect.
- taxonkit lca:
  - new flag -K/--keep-invalid: print the query even if no single valid taxid left. #89
TaxonKit v0.15.1
- taxonkit name2taxid:
  - remove the restriction of name types. #87
TaxonKit v0.15.0
- taxonkit reformat:
  - For lineages with more than one node, if it fails to query TaxId with the parent-child pair, use the last child only. #82
  - The flag -T/--trim also does not add the prefix for missing ranks lower than the current rank. #82
  - New flag -s/--miss-rank-repl-suffix to set the suffix for estimated taxon names. #85
TaxonKit v0.14.2
- taxonkit filter:
  - fix checking merged/deleted/not-found taxids. #80
- taxonkit lca:
  - add a new flag -b/--buffer-size to set the size of the line buffer. #75
  - fix typos: --separater -> --separater, the former is still available for backward compatibility.
- taxonkit reformat:
  - output compatible format for TaxIds not found in the database. #79
- taxonkit taxid-changelog:
  - support gzip-compressed taxdump files for saving space. #78
TaxonKit v0.14.1
- taxonkit reformat:
  - The flag -S/--pseudo-strain does not require -F/--fill-miss-rank now.
  - For taxa of rank >= species, {t}, {S}, and T outputs nothing when using -S/--pseudo-strain.
TaxonKit v0.14.0
- taxonkit create-taxdump:
  - save taxIds in int32 instead of uint32, as BLAST and DIAMOND do. #70
- taxonkit list:
  - do not skip visited subtrees when some of give taxids are descendants of others. #68
- taxonkit:
  - when environment variable TAXONKIT_DB is set, explicitly setting --data-dir will override the value of TAXONKIT_DB.
TaxonKit v0.13.0
- taxonkit reformat:
  - add a new placeholder {K} for rank kingdom. #64
  - do not panic for invalid TaxIds, e.g., the column name, when using -I--taxid-field.
- taxonkit create-taxdump:
  - fix merged.dmp and delnodes.dmp. Thanks to @apcamargo ! gtdb-taxdump/issues/2.
  - fix bug of handling non-GTDB data when using -A/--field-accession and no rank names given: the colname of the accession column would be treated as one of the ranks, which messed up all the ranks.
  - fix the default option value of --field-accession-re which wrongly remove prefix like Sp_. #65
- taxonkit list:
  - fix warning message of merged taxids.
TaxonKit v0.12.0
- taxonkit create-taxdump:
  - accepts arbitrary ranks #60
  - better handle of taxa with same names.
  - many flags changed.
TaxonKit v0.11.1
- taxonkit create-taxdump: fix bug of missing Class rank, contributed by @apcamargo. The flag --gtdb was not effected. #57
TaxonKit v0.11.0
- new command taxonkit create-taxdump: Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV. #56
TaxonKit v0.10.1
- taxonkit cami2-filter: fix option --show-rank which did not work in v0.10.0.
TaxonKit v0.10.0
- new command taxonkit cami2-filter: Remove taxa of given TaxIds and their descendants in CAMI metagenomic profile
- taxonkit reformat: fix panic for deleted taxid using -F/--fill-miss-rank. #55
TaxonKit v0.9.0
- new command taxonkit profile2cami: converting metagenomic profile table to CAMI format
TaxonKit v0.8.0
- taxonkit reformat:
  - accept input of TaxIds via flag -I/--taxid-field.
  - accept single taxonomy names.
  - show warning message for TaxIds with the same lineage. #42
  - better flag checking. #40
- taxonkit lca:
  - slightly speedup.
- taxonkit genautocomplete:
  - support bash|zsh|fish/powershell
TaxonKit v0.7.2
- taxonkit lineage:
  - new flag -R/--show-lineage-ranks for appending ranks of all levels.
  - reduce memory occupation and slightly speedup.
- taxonkit filter:
  - flag -E/--equal-to supports multiple values.
  - new flag -n/--save-predictable-norank: do not discard some special ranks without order when using -L, where rank of the closest higher node is still lower than rank cutoff.
- taxonkit reformat:
  - new placeholder {t} for subspecies/strain, {T} for strain. Thanks @wqssf102 for feedback.
  - new flag -S/--pseudo-strain for using the node with lowest rank as strain name, only if which rank is lower than "species" and not "subpecies" nor "strain".
TaxonKit v0.7.1
- taxonkit filter:
  - disable unnecessary stdin check when using flag --list-order or --list-ranks. #36
  - better handling of black list, empty default value: "no rank" and "clade". And you need use -N/--discard-noranks to explicitly filter out "no rank", "clade". #37
  - update help message. Thanks @standage for improve this command! #38
TaxonKit v0.7.0
- taxonkit: 2-3X faster taxonomy data loading.
- new command taxonkit filter: filtering TaxIds by taxonomic rank range. #32
- new command taxonkit lca: Computing lowest common ancestor (LCA) for TaxIds.
- taxonkit reformat:
  - new flag -P/--add-prefix: add prefixes for all ranks, single prefix for a rank is defined by flag --prefix-X, where X may be k, p, c, o, f, s, S.
  - new flag -T/--trim: do not fill missing rank lower than current rank.
- taxonkit list: do not duplicate root node.
TaxonKit v0.6.2
- taxonkit reformat -F: fix taxids of abbreviated lineage containing names shared by different taxids. #35
TaxonKit v0.6.1
- taxonkit lineage:
  - new flag -n/--show-name for appending scientific name.
  - new flag -L/--no-lineage for hide lineage, this is for fast retrieving names or/and ranks.
- taxonkit reformat:
  - fix flag -F/--fill-miss-rank.
  - discard order restriction of rank symbols.
TaxonKit v0.6.0
- taxonkit list:
  - check merged and deleted taxids.
  - fix bug of json output. #30
- taxonkit name2taxid: new flag -s/--sci-name for limiting to searching scientific names. #29
- taxonkit version: make checking update optional
TaxonKit v0.5.0
- 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.
TaxonKit v0.4.3
- taxonkit taxid-changelog: rewrite logic, fix bug and add more change types
TaxonKit v0.4.2
- taxonkit taxid-changelog: change output of ABSORB, do not merged into one record for changes in different versions.
TaxonKit v0.4.1
- taxonkit taxid-changelog:
  - add fields: name and rank.
  - and fix sorting bug.
  - detailed lineage change status
TaxonKit v0.4.0
- new command: taxonkit taxid-changelog: for creating taxid changelog from dump archive
TaxonKit v0.3.0
- this version is almost the same as v0.2.5
TaxonKit v0.2.5
- 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
- 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
- fix bug brought in v0.2.1
TaxonKit v0.2.2
- make verbose information optional #4
TaxonKit v0.2.1
- 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
- add command name2taxid to query taxid by taxon scientific name.
- lineage, reformat: changed flags and default operations, check the usage.
TaxonKit v0.1.8
- taxonkit lineage, add an extra column of lineage in Taxid. #3. e.g.,
- fix colorful output in windows.
TaxonKit v0.1.7
- taxonkit reformat: supports reading stdin from output of taxonkit lineage, reformated lineages are appended to input data.
TaxonKit v0.1.6
- remove flag -f/--formated-rank from taxonkit lineage, using taxonkit reformat can archieve same result.
TaxonKit v0.1.5
- reorganize code and flags
TaxonKit v0.1.4
- add flag --fill for taxonkit reformat, which estimates and fills missing rank with original lineage information
TaxonKit v0.1.3
- add command of taxonkit reformat which reformats full lineage to custom format
TaxonKit v0.1.2
- add command of taxonkit lineage, users can query lineage of given taxon IDs from file
TaxonKit v0.1.1
- 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
- first release