1.0.0

First release of TreeKnit, a Rust port of TreeKnit.jl, which infers reassortment from segment trees.

• MCCs: maximally compatible clades for every pair of trees, in the MCCs.json and MCCs.dat formats of TreeKnit.jl
• Resolution: polytomies resolved using the other trees (--resolve matched|strict|liberal|none)
• ARG: for two trees, an ancestral reassortment graph in extended Newick
• Different leaf sets: inference uses the leaves a pair shares, and leaves missing from one tree are imputed into it (--impute)
• Figures: --plot writes an SVG tanglegram of each pair and, for two trees, an SVG figure of the ARG
• Reproducible runs: --seed fixes the result, whatever the number of threads
• Input checks: every error in the trees and settings is reported before a run, one per line
• Web app: the same analyses in the browser at neherlab.github.io/treeknit. --session, --example, --link, and --print-link move an analysis between the web app and the command line
• Install:
  • prebuilt binaries for Linux, macOS, and Windows
  • pip install treeknit
  • conda install -c bioconda treeknit
  • docker pull neherlab/treeknit
• For users of TreeKnit.jl: the page for users of TreeKnit.jl lists every difference. The main ones:
  • the default resolution is matched for any number of trees
  • --gamma, --n-mcmc-it, --no-likelihood, and --seq-lengths take effect
  • the former method options still work
• Documentation: the command-line reference lists every option and output file

Downloads

🌐 Web app	neherlab.github.io/treeknit, runs in the browser without installation
⌨️ CLI	Linux x86_64 glibc musl* 6.7 MB 6.9 MB Linux ARM64 glibc musl* 6.3 MB 6.3 MB macOS** Apple Silicon executable 5.2 MB macOS** Intel executable 5.7 MB Windows x86_64 .exe 5.9 MB
🐍 Python (pip)	pip install treeknit==1.0.0 (PyPI)
🐍 Conda	conda install -c bioconda treeknit=1.0.0 (versions)***
🐋 Docker	docker pull neherlab/treeknit:1.0.0 (tags)
📂 Source code	github.com/neherlab/treeknit (f12a743)
🚩 Issues	Report bugs, suggest features

_{* glibc builds are recommended and need glibc 2.17 or newer. musl builds are static and run on any Linux distribution
** macOS executables are not signed by a registered developer. If macOS refuses to run one, run xattr -d com.apple.quarantine <file>
*** Bioconda releases need manual approval and can be delayed
On Linux and macOS, make the downloaded file executable with chmod +x <file>. The x86_64 builds need a Haswell (2013) or newer CPU, the Linux ARM64 builds an ARMv8.2-A CPU}

1.0.0-nightly.20261008T035529Z+04a4a2a

Warning

Nightly build of main for early testing. It may contain bugs and breaking changes.

Downloads

🌐 Web app	neherlab.github.io/treeknit-rs, runs in the browser without installation
⌨️ CLI	Linux x86_64 glibc musl* 5.1 MB 5.2 MB Linux ARM64 glibc musl* 4.7 MB 4.8 MB macOS** Apple Silicon executable 4.3 MB macOS** Intel executable 4.7 MB Windows x86_64 .exe 4.9 MB
📂 Source code	github.com/neherlab/treeknit-rs (04a4a2a)
🚩 Issues	Report bugs, suggest features

_{* musl builds are static and run on any Linux distribution. glibc builds need glibc 2.17 or newer
** macOS executables are not signed by a registered developer. If macOS refuses to run one, run xattr -d com.apple.quarantine <file>
On Linux and macOS, make the downloaded file executable with chmod +x <file>. The x86_64 builds need a Haswell (2013) or newer CPU, the Linux ARM64 builds an ARMv8.2-A CPU}

1.0.0-nightly.20261006T073611Z+f042155

Warning

Nightly build of main for early testing. It may contain bugs and breaking changes.

Downloads

🌐 Web app	neherlab.github.io/treeknit-rs, runs in the browser without installation
⌨️ CLI	Linux x86_64 glibc musl* 4.8 MB 5.0 MB Linux ARM64 glibc musl* 4.5 MB 4.5 MB macOS** Apple Silicon executable 4.0 MB macOS** Intel executable 4.4 MB Windows x86_64 .exe 4.7 MB
📂 Source code	github.com/neherlab/treeknit-rs (f042155)
🚩 Issues	Report bugs, suggest features

_{* musl builds are static and run on any Linux distribution. glibc builds need glibc 2.17 or newer
** macOS executables are not signed by a registered developer. If macOS refuses to run one, run xattr -d com.apple.quarantine <file>
On Linux and macOS, make the downloaded file executable with chmod +x <file>. The x86_64 builds need a Haswell (2013) or newer CPU, the Linux ARM64 builds an ARMv8.2-A CPU}

1.0.0-nightly.20261006T060541Z+4c3df81

Warning

Nightly build of main for early testing. It may contain bugs and breaking changes.

Downloads

🌐 Web app	neherlab.github.io/treeknit-rs, runs in the browser without installation
⌨️ CLI	Linux x86_64 glibc musl* 4.8 MB 5.0 MB Linux ARM64 glibc musl* 4.5 MB 4.5 MB macOS** Intel executable 4.4 MB Windows x86_64 .exe 4.7 MB
📂 Source code	github.com/neherlab/treeknit-rs (4c3df81)
🚩 Issues	Report bugs, suggest features

_{* musl builds are static and run on any Linux distribution. glibc builds need glibc 2.17 or newer
** macOS executables are not signed by a registered developer. If macOS refuses to run one, run xattr -d com.apple.quarantine <file>
On Linux and macOS, make the downloaded file executable with chmod +x <file>. The x86_64 builds need a Haswell (2013) or newer CPU, the Linux ARM64 builds an ARMv8.2-A CPU}

1.0.0-nightly.20261006T035258Z+5f70c3d

Warning

Nightly build of main for early testing. It may contain bugs and breaking changes.

Downloads

🌐 Web app	neherlab.github.io/treeknit-rs, runs in the browser without installation
⌨️ CLI	Linux x86_64 glibc musl* 2.0 MB 2.2 MB Linux ARM64 glibc musl* 1.9 MB 2.0 MB macOS** Apple Silicon executable 1.7 MB macOS** Intel executable 1.9 MB Windows x86_64 .exe 2.0 MB
📂 Source code	github.com/neherlab/treeknit-rs (5f70c3d)
🚩 Issues	Report bugs, suggest features

_{* musl builds are static and run on any Linux distribution. glibc builds need glibc 2.17 or newer
** macOS executables are not signed by a registered developer. If macOS refuses to run one, run xattr -d com.apple.quarantine <file>
On Linux and macOS, make the downloaded file executable with chmod +x <file>. The x86_64 builds need a Haswell (2013) or newer CPU, the Linux ARM64 builds an ARMv8.2-A CPU}

1.0.0-nightly.20261005T190347Z+04e1062

Warning

Nightly build of main for early testing. It may contain bugs and breaking changes.

Downloads

🌐 Web app	neherlab.github.io/treeknit-rs, runs in the browser without installation
⌨️ CLI	Linux x86_64 glibc musl* 2.0 MB 2.1 MB Linux ARM64 glibc musl* 1.9 MB 1.9 MB macOS** Apple Silicon executable 1.7 MB macOS** Intel executable 1.8 MB Windows x86_64 .exe 1.9 MB
📂 Source code	github.com/neherlab/treeknit-rs (04e1062)
🚩 Issues	Report bugs, suggest features

_{* musl builds are static and run on any Linux distribution. glibc builds need glibc 2.17 or newer
** macOS executables are not signed by a registered developer. If macOS refuses to run one, run xattr -d com.apple.quarantine <file>
On Linux and macOS, make the downloaded file executable with chmod +x <file>. The x86_64 builds need a Haswell (2013) or newer CPU, the Linux ARM64 builds an ARMv8.2-A CPU}