PhyloForester
Contents:
Installation
Installing Pre-built Binaries
Windows
macOS
Linux
Installing from Source
Prerequisites
Steps
Development Installation
Installing External Analysis Software
TNT (Parsimony Analysis)
IQTree (Maximum Likelihood)
MrBayes (Bayesian Inference)
Verifying Installation
Updating PhyloForester
Binary Installation
Source Installation
Uninstalling
Windows (Installer)
Windows (Portable) / macOS / Linux
Next Steps
User Guide
Getting Started
Main Window Overview
Working with Projects
Creating a Project
Editing Project Properties
Deleting a Project
Working with Datamatrices
Creating a New Datamatrix
Importing a Datamatrix
Editing a Datamatrix
Exporting a Datamatrix
Running Analyses
Creating an Analysis
Parsimony Analysis (TNT)
Maximum Likelihood (IQTree)
Bayesian Analysis (MrBayes)
Stopping an Analysis
Viewing Results
Analysis Output
Tree Visualization
Character Mapping
Advanced Features
Batch Operations
Database Management
Preferences
Keyboard Shortcuts
Tips and Best Practices
Organizing Projects
Data Quality
Analysis Settings
File Management
Next Steps
Analysis Guide
Overview
Choosing an Analysis Method
Parsimony
Maximum Likelihood
Bayesian Inference
Parsimony Workflow
Step 1: Prepare Data
Step 2: Create Parsimony Analysis
Step 3: Run Analysis
Step 4: Examine Results
Maximum Likelihood Workflow
Step 1: Prepare Data
Step 2: Model Selection
Step 3: Create ML Analysis
Step 4: Run Analysis
Step 5: Interpret Results
Bayesian Workflow
Step 1: Prepare Data
Step 2: Set Priors
Step 3: Configure MCMC
Step 4: Run Analysis
Step 5: Assess Convergence
Step 6: Examine Posterior
Character Mapping
Fitch Parsimony Mapping
Interpreting Mapped Trees
Comparing Analyses
Topology Comparison
Support Value Comparison
Troubleshooting Analyses
Analysis Won’t Start
Analysis Fails Immediately
Analysis Runs Forever
Poor Support Values
Best Practices
Data Preparation
Parameter Selection
Quality Control
Publication
Next Steps
Troubleshooting
Installation Issues
Application Won’t Start
Python Source Installation Fails
Data Management Issues
Can’t Open Database
Database Corruption
Import/Export Problems
File Won’t Import
Export Fails
Analysis Issues
External Software Not Found
Analysis Fails to Start
Analysis Runs but No Results
Analysis Takes Too Long
UI and Display Issues
Window Layout Broken
Trees Not Displaying
Text Too Small/Large
Keyboard Shortcuts Not Working
Datamatrix Editor Issues
Can’t Edit Cells
Undo/Redo Not Working
Copy/Paste Not Working
Performance Issues
Application Slow
Tree Rendering Slow
Error Messages
“Permission Denied”
“Out of Memory”
“Database Locked”
“Invalid Datamatrix”
Reporting Bugs
Getting Help
Next Steps
Developer Guide
Architecture Overview
Core Components
Setting Up Development Environment
Prerequisites
Clone Repository
Create Virtual Environment
Install Dependencies
Run from Source
Code Structure
Data Storage
Database Schema
Running Tests
Run All Tests
Run Specific Test File
Run with Coverage
Test Categories
Code Quality
Linting
Code Style
Type Hints
Contributing
Workflow
Commit Messages
Pull Request Guidelines
Building Documentation
Building Executables
Build Script
Manual PyInstaller
Platform-Specific Notes
Version Management
Update Version
Release Process
CI/CD Pipeline
Workflows
Manual Release
Adding Features
Adding a New Analysis Type
Adding a New Import Format
Extending the UI
Debugging
Logging
PyQt Debugging
Database Inspection
Resources
Contact
Next Steps
Changelog
[0.1.0] - 2025-11-03
Added
Changed
Fixed
[Pre-0.1.0] - Development Versions
Unreleased
Version History
See Also
PhyloForester
Index
Edit on GitHub
🌐
English
|
한국어
Index