BABAPPA GUI: A Codeml-Centered Positive Selection Analysis Software

Babappa is a Windows–WSL pipeline designed for large-scale evolutionary selection analysis. It integrates PAML (codeml), IQ-TREE, and custom workflows into three major pipelines: clip, clipgard, and normal. The software provides a Windows graphical interface that communicates with a backend FastAPI server running under WSL (Ubuntu-22.04). Technical features: Automated environment setup using Miniconda inside WSL. Reproducible environment creation from babappa_env.yml. Mamba solver preferred, with automatic fallback to conda. Startup script implements: environment auto-creation with retry logic, automatic acceptance of conda Terms of Service, handling of network instability and cache cleanup, MKL bug workarounds. User-local installation path (AppData\Local\Programs\Babappa), avoiding permission issues. Project files automatically copied into WSL home (~/babappa_project). Backend served by uvicorn/FastAPI, with logs stored under ~/.local/state/babappa/start.log and ~/babappa_uvicorn.log. Output organization: Results stored in C:\Users\<Username>\Documents\out\. Consistent folder structure across pipelines, including: codeml outputs (output.txt, rst, rub, etc.), likelihood ratio test summaries (LRT_results_lnL_np_values.xlsx, CSV files), IQ-TREE .treefile outputs, alignments (*.fas), per-step log files. Intended use:Babappa is intended for researchers conducting selection analysis in molecular evolution. It simplifies setup and execution by abstracting conda environment management, dependency resolution, and backend API startup into a seamless workflow accessible from a Windows GUI. Developer: Krishnendu SinhaContact: [email protected]