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 models
      • MacSyFinder’s functioning
    • Frequently Asked Questions
      • Frequently Asked Questions
  • Modeller Guide
  • Developer Guide
MacSyFinder
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User Guide

Running MacSyFinder

  • What’s new in MacSyFinder v2?
    • New features and search engine
  • 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
  • Installing models
    • How to install new models
    • Where the models are located
  • 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)

Frequently Asked Questions

  • Frequently Asked Questions
    • How to report an issue?
    • How to cite MacSyFinder and published macy-models?
    • What do MacSyFinder command lines look like?
    • What search mode to be used?
    • How to interpret the results from an unordered search?
    • How to search for multiple systems at once?
    • When can the option –previous-run be used?
    • Which output file to be used to get ONE solution?
    • Where to find MacSyFinder models?
    • What are the rules for options precedence?
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