Welcome to PanACoTA’s documentation!

If you use PanACoTA, please cite:

Amandine PERRIN, Eduardo P.C. ROCHA (2021). PanACoTA: a modular tool for massive microbial comparative genomics, NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021

User documentation

• What is PanACoTA
• Starting with PanACoTA
  • Installation
  • Quick run
• Running PanACoTA - help by module
  • General information
  • all subcommand
  • prepare subcommand
  • annotate subcommand
  • pangenome subcommand
  • corepers subcommand
  • align subcommand
  • tree subcommand
• Tutorial on examples
  • Genomes description
  • Annotate step
  • PanGenome step
  • Core/Persistent Genome step
  • Alignment step
  • Tree step
• About PanACoTA

Developer documentation

• Work on PanACoTA code
• PanACoTA API

Indices and tables

• Index

• Module Index

• Search Page