Contents

• Preface
  • Notational Conventions
  • Operating Systems
  
  
• List of Figures
• List of Tables
• Introduction
  • General Overview
    • Definition of the Problem
    • Experimental Design
    • Genetic Linkage Maps
  • Programming Philosophy
  • Copyright Information and Acknowledgments
    • QTL Cartographer Copyright Information
    • Citing QTL Cartographer
    • Gnuplot Copyright Information
    • LINPACK Copyright Information
    • Numerical Recipes in C Information
  • How to Get and Install QTL Cartographer
    • MS-Windows
    • UNIX
    • Macintosh
  • Getting Help
    • Mailing List
    • Bug Reports
    • Contacts
  • General Usage of the Programs
    • Options for all programs
    • Filenaming Conventions
  
  
• Simulating/Reformatting Data
  • Rmap
    • Simulating a Map
    • Using MAPMAKER/EXP files
    • QTL Cartographer user input format
    • Command Line Options
  • Rqtl
  • Rcross
    • Simulating Data
    • Translating Data
    • Output
  • Prune
    • Pruning Datasets Interactively
    • Recreating Datasets
  
  
• Analysis
  • Qstats
    • Command Line Options
    • Segregation
  • LRmapqtl
    • Simple Linear Regression
    • Output
    • Permutation Tests
  • SRmapqtl
    • Output
  • Zmapqtl
    • Computational Methodology
    • Models
    • Zmapqtl Options
    • Output
  • JZmapqtl
    • JZmapqtl Options
    • Output
    • Usage Hints
  • MImapqtl
    • MImapqtl Options
    • QTL Search
    • Epistatic Interactions
    • Threshold
  
  
• Visualization of Results
  • Eqtl
    • Options
  • Preplot
    • Printing Results
  • GNUPLOT
    • Basic GNUPLOT
  
  
• Tutorial Examples
  • General tactics and notes
    • Conventions
    • Text Files
    • Gnuplot
  • Basic Macintosh
  • Basic Windows
    • Navigating disks
    • Viewing files
    • Command Prompt
    • Transferring Files
  • Basic Unix
    • Help!
    • Basic filesystem commands
    • Other commands
  • Simulating and Analyzing data
  • Analyzing simulated data
  • Analyzing real data
  • Analyzing a MAPMAKER data set
    • Using MAPMAKER/EXP
    • Using the MAPMAKER files
  • Multiple Interval Mapping
    • Multiple interval mapping from scratch
    • Composite interval mapping preceeds multiple interval mapping
    • Multiple regression preceeds multiple interval mapping
    • Real Data
  • Multiple Trait Mapping
  
  
• Input File Formats
  • Genetic Linkage Maps
    • MAPMAKER output files
    • Rmap input files
    • Rmap output files
  • QTL information
    • Rqtl input files
    • Rqtl output files
  • Data files
    • MAPMAKER raw files
    • Rcross input files
  
  
• Benchmarks
• UNIX Man Pages
  • QTLCART
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • EXAMPLES
    • GLOBAL COMMAND LINE OPTIONS
    • GLOBAL BEHAVIOR
    • RESOURCE FILE
    • WORKING DIRECTORY
    • FILENAME STEM
    • USING THE INDIVIDUAL PROGRAMS
    • REFERENCES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • RMAP
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • EXAMPLES
    • REFERENCES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • RQTL
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • EXAMPLES
    • REFERENCES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • RCROSS
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • OUTPUT
    • CROSSES
    • EXAMPLES
    • REFERENCES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • PRUNE
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • AUTOMATIC ACTIONS
    • EXAMPLES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • QSTATS
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • EXAMPLES
    • REFERENCES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • LRMAPQTL
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • MODEL
    • INPUT FORMAT
    • EXAMPLES
    • REFERENCES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • SRMAPQTL
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • EXAMPLES
    • REFERENCES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • ZMAPQTL
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • EXAMPLES
    • MODELS
    • PERMUTATION TESTS
    • REFERENCES
    • CAVEATS
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • JZMAPQTL
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • EXAMPLES
    • MODELS
    • REFERENCES
    • BUGS
    • HINTS
    • SEE ALSO
    • CONTACT INFO
  • MULTIREGRESS
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • EXAMPLES
    • SEE ALSO
    • CONTACT INFO
  • MIMAPQTL
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • FILES
    • NOTES
    • EXAMPLES
    • REFERENCES
    • CAVEATS
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • PREPLOT
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • EXAMPLES
    • REFERENCES
    • CAVEATS
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  • EQTL
    • NAME
    • SYNOPSIS
    • DESCRIPTION
    • OPTIONS
    • INPUT FORMAT
    • EXAMPLES
    • BOOTSTRAPS, JACKKNIVES AND PERMUTATIONS
    • REFERENCES
    • BUGS
    • SEE ALSO
    • CONTACT INFO
  
  
• Bibliography
• Index
• About this document ...