Welcome to Orthoflow’s documentation!

Contents:

• Installation
  • Conda Installation
  • pip Installation
  • Source Installation
• Beginner Tutorial
  • Input data
  • Simple run
  • Examining the output
• Advanced Tutorial
  • Changing workflow settings
  • Cores
  • Setting working directory and specifying targets
  • Controlling the flow of operations
  • Gene and alignment filtering settings
  • Tree inference settings
• Reproduction Tutorial
  • Downloading the data
  • Setup
  • Running Orthoflow
  • Results
  • Mini Test
• One Thousand Plant Transcriptomes Tutorial
  • Downloading and Input File Creation
  • Config
  • Running Orthoflow
• Input
• Workflow
  • Data Intake Module
  • Orthofisher Module
  • Orthofinder Module
  • Alignment Module
  • Supermatrix Module
  • Gene Tree Module
  • Supertree Module
  • Report Module
• Contributing
  • Testing
  • Git Commits
  • Documentation
  • Code of Conduct
• Citation and Attribution
  • Bibliography

Indices and tables

• Index

• Snakemake Rules

• Module Index

• Search Page