BABAPPA GUI: A Codeml-Centered Positive Selection Analysis Software

AbstractBABAPPA GUI is a user-friendly graphical front end for a Codeml-dependent positive selection analysis pipeline. It packages three analysis workflows (clip, clipgard, and normal) that wrap alignment QC, tree inference, site- and branch-model Codeml runs, multiple test corrections and result aggregation. The GUI launches a FastAPI backend inside WSL (Ubuntu 22.04) to run the core pipeline and provides a straightforward ‘Quick Start’ for non-expert users while retaining advanced manual controls for experienced operators. Key features Intuitive GUI to run Codeml-based positive selection analyses without extensive command-line work. Three built-in flavours: clip, clipgard, and normal. Automated environment deployment inside WSL (Ubuntu-22.04) using a packaged conda environment. Exports detailed results suitable for publication: LRT tables, Codeml outputs, phylogenetic trees, alignments and per-step logs. Developer-friendly: PyInstaller-based GUI build, conda-pack environment artifact, and Inno Setup installer script for Windows packaging. Contents of this release This Zenodo record provides the official installer and release artifacts for BABAPPA GUI: Windows installer (≈ 1.5 GB) — packaged installer for Windows (bundled Miniconda + WSL-friendly launcher). Source build artifacts and packaged conda environment (where applicable). Project README and supporting documentation (Quick start, troubleshooting, developer notes). Quick start (overview) Install — Download and run the Babappa installer (BabappaInstaller.exe) as Administrator; the default install path is C:\Program Files (x86)\Babappa. Launch — Open the Babappa GUI. On first run the GUI will provision the WSL environment and start a FastAPI backend in Ubuntu-22.04. Wait until the GUI log indicates the background API is running. The initial setup for the first run may take up to 30 minutes. Run analysis — Choose a FASTA input, output folder, pipeline (clip, clipgard, normal) and click Run Analysis. Clear Session — It resets the current analysis state, removes temporary files, and prepares the GUI for a fresh run without affecting saved results. Requirements Windows 10/11 (64-bit) WSL 2 with Ubuntu-22.04 installed and initialized ~5–10 GB free disk space (for environment + results) Typical result layout Each run produces a UUID-named folder under your chosen output directory with consistent subfolders: BHanalysis/, BHanalysis4sitemodel/, codemlanalysis/, codemloutput/, foregroundbranch/, iqtreeoutput/, logs/, msa/, sitemodel/, sitemodelanalysis/, treefiles/ Key files for publication: BHanalysis/LRT_results_lnL_np_values.xlsx, BHanalysis4sitemodel/lrt_results.csv, codemloutput/* (full PAML/Codeml outputs), iqtreeoutput/*.treefile, and msa/*.fas. Troubleshooting (common fixes) If the GUI reports “API did not start”: ensure WSL Ubuntu-22.04 is installed and the default WSL distro. (wsl -l -v) Conda TOS error: accept non-interactive terms inside WSL:conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main Permission errors: fix ownership inside WSL:sudo chown -R $(whoami):$(whoami) ~/babappa_project && chmod -R u+w ~/babappa_project Kill stale backend: pkill -f "uvicorn babappa_api:app" || true For full debugging, provide the last ~200 lines of ~/babappa_uvicorn.log. Developer / build notes GUI built with PyInstaller (--onefile --windowed), icon and installer script provided. Conda environment is packaged (conda pack); update and re-pack for new releases. Use Inno Setup Compiler with babappa_installer.iss for Windows installer generation. Installer hosting & verification Installer hosting: The official installer (~1.5 GB) for this release is hosted on Zenodo: 10.5281/zenodo.17211886. Verify integrity: After download, verify the installer checksum (SHA256). Example on Linux/macOS:sha256sum BabappaInstaller.exeOn Windows (PowerShell):Get-FileHash .\BabappaInstaller.exe -Algorithm SHA256 Contact & support Developer: Krishnendu SinhaEmail: [email protected]