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PyMS
by PyMS
What PyMS is
PyMS is a free, GPL-3.0 desktop application for visualizing and analyzing quantitative mycorrhizal fungi colonization in plant roots. It is designed for researchers who prefer a graphical interface instead of command-line software or want a more productive analysis workflow. PyMS reads a specifically formatted CSV containing colonization data measured with a modified grid-line intersect method or an equivalent approach. Users can select grouping and color parameters, generate a figure, and save it. Statistical options include Mann–Whitney tests for two genotypes and Kruskal–Wallis tests with Dunn post-hoc tests for multiple genotypes. Resulting p-values are written to a text file in the input CSV’s folder. The application runs on Linux, macOS, and Windows. Installation uses pip with the package name pyms-plot, followed by command-line launching. Python 3 and dependencies including pandas, NumPy, matplotlib, SciPy, statsmodels, and TkInter are required.
Who it suits
PyMS suits plant researchers analyzing mycorrhizal colonization data who want a graphical workflow. It is intended for users working with the required CSV format on Linux, macOS, or Windows.
What it does well
- Graphical interface for colonization analysis
- Mann–Whitney and Kruskal–Wallis testing
- Saves figures and p-values
- Runs on Linux, macOS, and Windows
- GPL-3.0 licensed free software
What to know first
- Accepts only specifically formatted CSV input
- Requires Python 3 and multiple dependencies
- No regression models or scripting support
Plans
| Plan | Billed and limits | Price |
|---|---|---|
| PyMS | Open-source GPL-3.0 software · requires Python 3 and dependencies · formatted CSV input | Free |
As pyms-jschnab.readthedocs.io lists them, read 9 Oct 2026. The maker's own page has the final word.
Verdict
PyMS focuses on a defined mycorrhizal colonization workflow, combining visual output with nonparametric statistical tests. Its strict CSV format and Python dependency stack should be checked before adoption.
Facts from PyMS's own pages
- Audience
- It is intended to help researchers unfamiliar with command-line software or seeking to increase productivity during data analysis. · pyms-jschnab.readthedocs.io, 9 Oct 2026
- Bayesian analysis
- No · pyms-jschnab.readthedocs.io, 23 Sept 2026
- Data import formats
- CSV · pyms-jschnab.readthedocs.io, 23 Sept 2026
- Dependencies
- The repository lists Python 3, pandas, NumPy, matplotlib, SciPy, statsmodels, and TkInter as dependencies. · github.com, 9 Oct 2026
- Deployment
- desktop · pyms-jschnab.readthedocs.io, 23 Sept 2026
- Founded
- 2019 · pyms-jschnab.readthedocs.io, 19 Oct 2026
- Free plan
- Yes · pyms-jschnab.readthedocs.io, 23 Sept 2026
- Input limit
- Input must be a specifically formatted CSV file containing colonization data quantified with a modified grid-line intersect method or an equivalent method. · pyms-jschnab.readthedocs.io, 9 Oct 2026
- Installation
- The repository documents installation with pip using the package name pyms-plot and running PyMS from the command line. · github.com, 9 Oct 2026
- Integrations
- The repository lists pandas, NumPy, matplotlib, SciPy, statsmodels, and TkInter as dependencies; it does not describe third-party service integrations. · github.com, 9 Oct 2026
- License
- The GitHub repository identifies the project as GPL-3.0 licensed. · github.com, 9 Oct 2026
- Output
- Statistical test p-values are saved to a text file in the same folder as the input CSV. · pyms-jschnab.readthedocs.io, 9 Oct 2026
- Purpose
- PyMS is a graphical interface for visualizing quantitative mycorrhizal fungi colonization of plant roots and analyzing the data. · pyms-jschnab.readthedocs.io, 9 Oct 2026
- Regression models
- No · pyms-jschnab.readthedocs.io, 23 Sept 2026
- Release
- The PyPI project page lists version 0.9.1, released April 17, 2019. · pypi.org, 9 Oct 2026
- Scripting support
- No · pyms-jschnab.readthedocs.io, 23 Sept 2026
- Security
- The opened documentation and repository pages do not state security certifications or compliance claims. · github.com, 9 Oct 2026
- Statistical tests
- Yes · pyms-jschnab.readthedocs.io, 23 Sept 2026
- Statistics
- It supports Mann–Whitney tests for two genotypes and Kruskal–Wallis tests followed by Dunn post-hoc tests for multiple genotypes. · pyms-jschnab.readthedocs.io, 9 Oct 2026
- Support
- The documentation directs users with questions to email [email protected]. · pyms-jschnab.readthedocs.io, 9 Oct 2026
- Visualization
- Users can choose grouping and color parameters, analyze a CSV file, and save the generated figure. · github.com, 9 Oct 2026
Where PyMS stands on Freedom251
- Statistical Analysis Software#35 of 106