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• Readme

  • Documentation
  • Installation
  • Quick Start
  • ab12phylo-cmd example
  • Dependencies
  • References

• Installation

  • Instructions
    • a) quick installation on windows
    • b) install to existing conda environment
    • c) tailor a conda environment for AB12PHYLO
    • d) install via pip to system python3
    • e) build from source via git and pip
    • f) install to conda via pip
  • Updating

• Commandline Tutorial

  • Basic options
  • Test run
  • Config files
  • More detailed settings
  • Run modes
  • BLAST
  • Results + Motif Search
  • Plotting
  • Troubleshooting / Odds and Ends

• Graphical Tutorial

  • Define a Dataset
  • Filename Parsing
  • ABI trace quality control
  • Build single-gene MSAs
  • Trim MSAs
  • BLAST
  • ML tree re-construction trace quality control
  • Tree plotting and population genetics