User Guide

Running MacSyFinder

• What’s new in MacSyFinder v2?
  • V 2.1.4
  • V 2.1.3
  • Features
  • V 2.1.1
  • V 2.1
  • 2.0
• Installation
  • MacSyFinder dependencies
  • MacSyFinder Installation procedure
  • Models installation with macsydata
• MacSyFinder Quick Start
• An example data set
• Input and Options of MacSyFinder
  • Input dataset
  • Command-line options
  • Configuration file
  • In-house input files
• Output format
  • Output files for the “ordered replicon(s)” search modes
  • all_systems.txt
  • all_systems.tsv
  • best_solution.tsv and all_best_solutions.tsv
  • best_solution_summary.tsv
  • best_solution_loners.tsv
  • best_solution_multisystems.tsv
  • rejected_candidates.txt
  • rejected_candidates.tsv
  • Output files for the “unordered replicon” search mode
  • all_systems.txt
  • all_systems.tsv
  • uncomplete_systems.txt
  • Hmmer results’ output files
  • Logs and configuration files
• For big data people
  • Parallelization

MacSyFinder functioning

• Macromolecular models
• Installing models
  • How to install new models
  • Where the models are located
• MacSyFinder’s search engine
  • 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 deal with fragmented genomes (MAGs, SAGs, draft genomes)?
  • 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?