Command-Line Interface (CLI) Guide

FastConformation provides command-line tools for performing various tasks such as MSA generation, ensemble prediction, and analysis. This section provides more detailed documentation for each CLI script.

CLI Tools

• MSA Generation Tool Documentation
• JackHMMeR Multiple Sequence Alignment
  • Overview
  • Usage
  • Example
• mmseqs2 Multiple Sequence Alignment
  • Overview
  • Usage
  • Example
• Configuration Files
• Output
• Ensemble Prediction
  • Command-Line Arguments
  • Usage Examples
• Command-Line Interface (CLI) Usage
  • Running 2D TM-Score Analysis
  • Running 1D TM-Score Analysis
  • Running 2D RMSD Analysis
  • Running 1D RMSD Analysis
  • Running RMSF Analysis
• Configuration

Overview

Below, you’ll find documentation for each tool, including the command-line arguments, usage examples, and best practices.

Available CLI Tools

• MSA Generation:

  The msa script handles Multiple Sequence Alignment (MSA) generation using tools like jackhmmer and mmseqs2.

• Ensemble Prediction:

  The predict_ensemble script is used for making ensemble predictions based on the generated MSAs.

• Analysis:

  The analysis script provides tools for analyzing the predicted structures, including RMSD and TM-score calculations, PCA clustering, and more.