User Guide

Using MacSyLib

• What’s new in MacSyLib
  • V 1.0
• Installation
  • MacSyLib dependencies
  • MacSyLib Installation procedure
  • Models installation with msl_data
• MacSyLib Quick Start
• Input and Options of MacSyLib
  • Input dataset
  • Config object
  • 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

MacSyLib functioning

• Macromolecular models
• Installing models
  • How to install new models
  • Where the models are located
• MacSyLib’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 MacSyLib and published macy-models?
  • How to use MacSyLib ?
  • 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?
  • Where to find MacSyLib models?
  • What are the rules for options precedence?