MacSyFinder
  • User Guide
    • Running MacSyFinder
      • What’s new in MacSyFinder v2?
      • Installation
      • MacSyFinder Quick Start
      • Input and Options of MacSyFinder
      • Output format
    • MacSyFinder functioning
      • Macromolecular models
      • Installing and sharing models
      • MacSyFinder’s functioning
  • Developer Guide
MacSyFinder
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User Guide¶

Running MacSyFinder¶

  • What’s new in MacSyFinder v2?
    • New features and search engine
    • Dependencies
    • Carrying models from v1 to v2
  • Installation
    • MacSyFinder dependencies
    • MacSyFinder Installation procedure
    • Models installation with macsydata
  • MacSyFinder Quick Start
  • Input and Options of MacSyFinder
    • Input dataset
    • Command-line options
    • Configuration file
    • In-house input files
  • Output format
    • Hmmer results’ output files
    • Output files for the “ordered replicon(s)” search modes
    • Output files for the “unordered replicon” search mode
    • Logs and configuration files

MacSyFinder functioning¶

  • Macromolecular models
    • Structure of a macsy-model package
    • Principles, and how to write macsy-models definitions
  • Installing and sharing models
    • How to install new models
    • Where the models are located
    • Writing my own macsy-model package
    • Share your models
  • MacSyFinder’s functioning
    • Functioning overview
    • A. Searching for Systems’ components
    • B. Hits browsing
    • C. Computing candidate Systems’ scores (ordered mode)
    • D. Repeat operations B and C for the other models being searched
    • E. Computing possible Solutions, defining the best one (ordered mode)
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