phymlGUI

English | Русский

Open-source desktop tool for building maximum-likelihood phylogenetic trees from FASTA files. It aligns unaligned sequences with MUSCLE, runs PhyML (serial or MPI) or IQ-TREE (ModelFinder, ultrafast bootstrap) and shows the tree in an interactive viewer. Single files or whole folders, with a run history and parameter presets. Ready-to-run packages for Windows and Linux with all analysis programs included. English/Russian interface, dark and light themes.

Features

1. Analysis pipeline

• Two engines: PhyML 3.3 (serial or parallel through MPI) and IQ-TREE 2 (automatic model selection with ModelFinder, ultrafast bootstrap), switchable in Settings.
• Alignment on the fly: unaligned FASTA is detected and aligned with MUSCLE before the analysis; aligned files go straight to the engine.
• Input checks before the run: IDs are cleaned and checked for collisions, FASTA is converted to relaxed PHYLIP, and invalid settings (a missing program, an MPI-only build without MPI, bad numbers) are listed together before anything starts.
• Parallel computing: MPI through mpiexec (Microsoft MPI, Windows) or mpirun (OpenMPI, Linux); the core count is pre-filled from the physical cores.
• Live CPU monitor: the status bar shows the system load and the load of the analysis process tree.
• Safe cancel: Cancel stops the whole process tree (mpiexec and every PhyML rank).

2. Tree viewer

• Layouts: rectangular, slanted and circular, with a distance grid and a scale in substitutions per site.
• Supports: bootstrap / aLRT / UFBoot values on branches, highlighting by a threshold.
• Editing the view: clade collapsing, rerooting on an outgroup, zoom and pan.
• Comparison: majority-rule consensus from bootstrap trees and Robinson–Foulds distance between two topologies.
• Export: PNG, SVG and PDF.

3. IQ-TREE with ModelFinder

• Model selection: MFP lets ModelFinder choose the substitution model; the chosen model, log-likelihood, gamma shape and run time appear in the Statistics tab.
• Ultrafast bootstrap: UFBoot supports on the tree; fewer than 1000 replicates (the UFBoot minimum) are raised to 1000 with a warning.

4. Batch mode, history and presets

• Batch mode: a whole folder of FASTA files in one run, with a live per-file queue, statuses, retry of the failed files and an N/M summary.
• Reports: phymlgui_summary.csv and phymlgui_summary.xlsx with the model, taxa, log-likelihood, gamma, Ts/Tv and run time of every file.
• Run history: every run is recorded with its parameters; a double click reopens its tree.
• Presets: built-in and user parameter presets, stored together with the engine.

5. Command line

The same pipeline without the window, for scripts and servers:

phymlgui-cli.exe --file data.fasta                  # Windows package
./phymlGUI-2.0.0-x86_64.AppImage --batch folder/    # Linux package
python phymlgui.py --file data.fasta --config preset.json

Settings come from the data folder; --config is a JSON object laid over them. Exit codes: 0 success, 1 a file failed or the run was cancelled, 2 a usage or input problem.

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Download

Ready-to-run packages are on the Releases page; Python is not required.

• Windows 10/11, 64-bit: phymlGUI-<version>-windows-x64.zip. Unpack the whole archive and run phymlgui.exe (phymlgui-cli.exe for the command line). PhyML needs Microsoft MPI (msmpisetup.exe), also for serial runs: the bundled PhyML is an MPI build.
• Linux x86_64: phymlGUI-<version>-x86_64.AppImage. Run chmod +x phymlGUI-*.AppImage and start it; without FUSE add --appimage-extract-and-run. Built on Ubuntu 22.04 (glibc 2.35 or newer). MPI mode needs OpenMPI: sudo apt install openmpi-bin.
• Checksums: SHA256SUMS, verify with sha256sum -c SHA256SUMS.

Bundled programs (in bin/, licences in licenses/):

Program	Windows	Linux
PhyML	3.3, MPI build	3.3.20260528, serial and MPI builds
IQ-TREE	2.4.0	2.4.0
MUSCLE	5.3	5.3
RAxML-NG	2.0.3, native build	2.0.3

RAxML-NG is included for use from the command line; an engine for it in the window is planned. The Windows build is made from the official sources with a small patch; the sources and the patch are attached to every release (AGPL-3.0).

Settings and history are kept next to the program when that folder is writable, otherwise in %APPDATA%\phymlGUI (Windows) or ~/.config/phymlGUI (Linux, $XDG_CONFIG_HOME). PHYMLGUI_DATA_DIR selects another folder.

Installation & Quick Start (from source)

Requires Python 3.11+ (3.12+ on Linux: with 3.11 the interpreter aborts on exit, bool_dealloc, because of a reference-count bug in a C extension).

python -m venv .venv
source .venv/bin/activate          # Windows: .venv\Scripts\activate
pip install -r requirements.txt
python scripts/fetch_third_party.py --dest bin   # pinned, SHA256-verified programs
python phymlgui.py

Programs are looked up in bin/ next to the app, then on PATH; paths can also be set in Settings.

Run the tests:

pip install -r requirements-dev.txt
python -m pytest

Tests that need a missing program are skipped; PHYMLGUI_PHYML, PHYMLGUI_MPIEXEC, PHYMLGUI_IQTREE, PHYMLGUI_MUSCLE and PHYMLGUI_RAXML point them to specific executables. The tests never touch your real settings. scripts/make_screenshots.py regenerates the screenshots from real runs.

Output files

Next to each input file:

• *_aligned.fasta: the MUSCLE alignment (for unaligned input)
• *.phy: the relaxed PHYLIP passed to the engine
• *_phyml_tree.txt, *_phyml_stats.txt, *_phyml_boot_trees.txt: PhyML results
• *.treefile, *.iqtree, *.log: IQ-TREE results
• phymlgui_summary.csv, phymlgui_summary.xlsx: one row per file

Citation

If you use phymlGUI in published work, please cite the programs that did the analysis:

• PhyML: Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 59(3):307–321, 2010.
• IQ-TREE 2: Minh BQ, Schmidt HA, Chernomor O, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37(5):1530–1534, 2020.
• MUSCLE 5: Edgar RC. Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nature Communications 13:6968, 2022.

License

MIT License — Copyright (c) 2026 Aleksey Drobin (@adrobi). The bundled programs keep their own licences: PhyML and MUSCLE GPL-3.0, IQ-TREE GPL-2.0, RAxML-NG AGPL-3.0 (see licenses/ in the packages). Changes are listed in CHANGELOG.md.