https://github.com/husonlab/phylocompare
PhyloCompare
https://github.com/husonlab/phylocompare
comparison parallelograms phylogenetics trees
Last synced: 19 days ago
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PhyloCompare
- Host: GitHub
- URL: https://github.com/husonlab/phylocompare
- Owner: husonlab
- License: other
- Created: 2026-01-13T12:35:14.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2026-06-06T08:07:43.000Z (22 days ago)
- Last Synced: 2026-06-06T09:20:49.064Z (22 days ago)
- Topics: comparison, parallelograms, phylogenetics, trees
- Language: Java
- Homepage: https://husonlab.github.io/phylocompare/
- Size: 3.14 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# PhyloCompare
PhyloCompare is an interactive desktop application for comparing rooted phylogenetic trees.
It provides a new visualization called a phylogenetic parallelogram, in which
multiple trees are drawn in parallel in the same coordinate space. This highlights shared evolutionary
structure while making conflicting signals immediately visible.
Phylogenetic parallelogram
## Features
- Compare multiple rooted phylogenetic trees interactively
- Compute and display phylogenetic parallelograms
- Visualize dozens of trees simultaneously
- Explore tree disagreement across loci or genomic regions
- Interactive zooming, panning, and selection
- Export high-quality figures for publication
- Available for macOS, Windows, and Linux
## Installation
Download the latest release from:
https://github.com/husonlab/phylocompare/releases/latest
### macOS
Download the installer matching your processor:
- Apple Silicon (M1/M2/M3/...): macOS ARM64
- Intel Macs: macOS Intel
Open the downloaded DMG file and drag PhyloCompare into the Applications folder.
### Windows
Download and run the MSI installer.
### Linux
Download either:
- the Debian package (.deb)
- or the portable archive (.tar.gz)
The portable archive can be unpacked and run without administrator privileges.
## Getting Started
1. Launch PhyloCompare.
2. Open a file containing rooted phylogenetic trees.
3. Select the trees to compare.
4. Explore areas of agreement and disagreement among the trees.
## Documentation
The complete user manual is available here:
[User Manual](https://husonlab.github.io/phylocompare/manual.html)
## Citation
If you use PhyloCompare in your research, please cite:
Daniel H. Huson, Banu Cetinkaya and Louxin Zhang. PhyloCompare: visualizing agreement and conflict among trees as
phylogenetic parallelograms. (Manuscript in preparation).
## License
PhyloCompare is distributed under the GNU General Public License v3 (GPL v3).
## Contact
Daniel H. Huson
University of Tübingen
Institute for Bioinformatics and Medical Informatics