| About Windows QTL Cartographer |
 | WinQTLCart features |
| Compatible programs and formats |
| System requirements |
| Installing, uninstalling, upgrading |
| Using WinQTL - a high-level overview |
| When to use WinQTLCart |
| WinQTLCart Windows & Menus |
| Main window tour |
| Main window - Tree Pane |
| Main window - Form Pane |
| Main window - Data Pane |
| Main window - Menus |
| Main window - Menus - File |
| Main window - Menus - Edit |
| Main window - Menus - View |
| Main window - Menus - Method |
| Main window - Menus - Tools |
| Main window - Menus - Help |
| Chromosome graph display - Menus |
| Chromosome graph - Menus - File |
| Chromosome graph - Menus - View |
| Chromosome graph - Menus - Setting |
| Restul Graph window - Menus |
| Graph window - Menus - File |
| Graph window - Menus - Chrom |
| Graph window - Menus - Traits |
| Graph window - Menus - Effects |
| Graph window - Menus - Tools |
| Graph window - Menus - Setting |
| One-page display window - Menus |
| One-Page window - Menus - File |
| One-Page window - Menus - View |
| One-Page window - Menus - Setting |
| Graph window - Procedures |
| Tracing coordinates on the graph |
| Selecting traits for graph display |
| Selecting chromosomes for graph display |
| Setting display parameters |
| Setting a test hypothesis |
| Showing QTL information |
| WinQTLCart Procedures |
| Setting the working directory |
| Importing and exporting |
| Importing files |
| Exporting source data and results |
| Exporting source data to QTL Cartographer |
| Exporting source data to an MCD file |
| Exporting results from the Graph window |
| Working with source data files |
| Opening source data files |
| View source data file's marker genotype data |
| View source data file's traits values |
| View source data file's other trait values |
| Manipulate source data file information |
| Basic information |
| Individual information |
| Chromosome and marker information |
| Trait information |
| Other trait information |
| MCD file format |
| Creating a new source data file from raw data |
| Step 1 - Basic Information |
| Step 2 - Mpa Information 1 |
| Step 3 - Map Information 2 |
| Step 4 - Cross Information 1 |
| Step 5 - Cross Information 2 |
 | Step 6 - View and Finish |
| Creating simulation data |
| Single-marker analysis |
| Setting threshold levels (IM & CIM) |
| Setting threshold levels manually |
| Setting threshold levels via permutations |
| Interval Mapping |
| Running interval mapping analysis |
| Composite Interval Mapping |
| Running composite interval mapping analysis |
| Multiple Interval Mapping |
| About the MIM form |
| Creating MIM initial model |
| Regression options |
| CIM search option |
| MIM search option |
| Refining the MIM model |
| Optimizing QTL positions for MIM |
| Searching for new QTLs-MIM |
| Testing for existing QTLs |
| MIM model summary |
| Bayesian Interval Mapping |
| Running Bayesian interval mapping analysis |
| Multiple-trait analysis |
| Category trait analysis |
| Drawing a chromosome tree |
| Adding QTL positions to the chromosome graphics |
| Tutorials |
| Import data files |
| Import data - INP format |
| Using Emap function |
| Import data - OUT format |
| Import data - MapMaker format |
| Import data - Excel format |
| Simulation source data file |
| Create new source data file |
| Single marker analysis |
| Interval mapping |
| Composite interval mapping |
| Multiple-trait analysis |
| Multiple Interval Mapping |
| Bayesian interval mapping |
| Result manipulation |
| Technical notes |
| Troubleshooting |
| WinQTLCart cannot import Map information from selected file |
| Invalid file or wrong format messages |
| Technical Support |
| Credits & acknowledgements |