Documentation
MateSel and MateSel Legacy Versions
The documentation below applies to the MateSel Legacy version only. The new version of MateSel (as pictured throughout this new website) will be released in the coming weeks with it's own dedicated documentation website. An annoucement will be made when it is released.
MateSel Legacy Instructions
A guide on all MateSel Legacy features
Video Series
The MateSel video series is hosted on YouTube. Click here or the YouTube logo to view the MateSel YouTube channel. An index of all videos can be found below.
Category 1: Introduction
| General Introduction | A quick introduction to how MateSel works and its core functions and features. |
| Overview and Demo Project Test Drive | Provides a walkthrough of a demo project that comes with MateSel. |
Category 2: Preparing your data files
| Preparing your main data file | Comprehensive, except no detail on handling genetic markers. |
| Preparing Matesel.ini | Please also see Introduction to version 7&12.9 from about 6min, which shows the new format for Matesel.ini, including automatic upgrading. |
| Preparing InpOneGroup.txt | Setting constraints and other settings across all candidates. Includes basic discussion on what Groups are in MateSel. |
| Preparing InpGroups.txt - Standard Operations | Everything in this file up to the permission matrix, except for 'natural mating'. Example in beef cattle across US states. |
| Preparing InpGroups.txt - Advanced Operations | Features below the permission matrix in this file, plus 'natural mating'. Some discussion on method used for Grouping. |
Category 3: The MateSel user interface
| Windows Desktop | Coming soon… |
| Batch Versions | Coming soon… |
Category 4: The MateSel Frontier
| Frontier fundamentals | Includes discussion of what parental coancestry is, and why relationships are important. Simple spreadsheet example. Desired outcomes discussion, including programs Desire and Diversity. |
| Where should I aim? | First, be sure to make a correct Frontier – by example. Your corporate position. Measuring and predicting inbreeding rate/diversity loss and its effect on long-term gains. |
| Working with Balance Strategies | First 4 mins is introduction – you could fast forward that. Walking through the different ways of balancing Progeny Index and Parental Coancestry, with discussion on what strategy might be most suitable. |
Category 5: Managing Trait Distributions
| Standard operations | What are these trait distributions? Worked example of using the different control types for manipulating traits. |
| Advanced operations | This includes a number of unusual tricks, eg showing distributions for sires and for dams, as well as for progeny. Also using dummy traits to manage ages, breed crossing, locations etc. Please also see Introduction to version 7.0.12.0 for the desired gains options when Committed Matings are being displayed, and also for some relevant updates to format of Matesel.ini. |
| Should I manage my traits? | Changing distribution means (responses), and shapes (eg variances). Managing genetic variation for individual traits, and planning for the splitting of breeding lines. Discussion on compromises caused by mating for desired trait distribution shapes. |
Category 6: Genetic markers
| Coding markers in the main data file | This video tells you how to enter genetic marker data into your dataset, so that you can manipulate these in Matesel. |
| Managing individual markers/QTL/Gene Edits | A guide to how marker information is displayed and how to use Matesel to manage allele and genotype distributions in the progeny. |
| Managing sex-linked markers | How to set up a sex-linked marker in your main data file, and manage it in your Matesel analysis. |
| Managing Recessive Lethals and Gene Edits collectively | How to handle many markers in a collection – for multiple Recessive Lethals or for multiple Gene Edits. |
| The Genomic Relationship Matrix | Make your GRM and use it in Matesel. Automatic imputation of missing relationships; controlling how Matesel uses your GRM; using this facility to target specific genomic regions and for Genomic Mate Selection. Some discussion on calculating relationships. |
Category 7: Effective use of MateSel
| Working with weightings to achieve the best outcomes | Coming Soon… |
| Working dynamically with output files | Coming Soon… |
| Import your own solution | For an example see from about 3:36 minutes here: Where should I aim? |
| Diagnosis of convergence | MateSel uses an Evolutionary Algorithm to find a good solution. When should it stop looking? This video describes how to track and control convergence in your MateSel job, so that it will stop automatically at a good level of convergence. |
| Shortcut commands | Coming Soon… |
| Troubleshooting | Coming Soon… |
Category 8: Mixed Mating Groups
| Mixed Mating Groups | Under Mixed Mating Groups, multiple groups of males and females are selected either for mating within these mixed groups, or for initial cohorting to be followed by controlled mating at a later stage. Applications include: Multi-sire joining in beef and sheep, mass spawning in fish and shrimp, open pollination in plants and managing selection and migration of cohorts of animals across breeding units in a large operation. |
| Pre-assigned Groups and Shared Grouping under Mixed Mating Groups | How to pre-assign which individuals can be candidates for each of your Mixed Mating Groups for your species of animals or plants. As examples: We organise that heifers and cows are channelled into specific MMGs to be mated with groups of bulls with appropriate attributes. We illustrate control of selection and migration of both juveniles and breeding stock/semen across breeding and production units in pigs. |
| Accommodating variable male reproductive success | When males within a group compete for mating of females, their success rates can vary a lot, and this increases Parental Coancestry, leading to damaging effects on genetic diversity. This is a technical video that describes our method to correct for this effect when running Mixed Mating Groups in MateSel. The results seem to be robust across different numbers of males and across the different species tested, all for the same calibration parameters. However, we tell you how to make your own fit for your own scenario. |
Category 9: Other Videos
| Multiple EndUses | Target customer needs as well as your own. Conceptual examples in beef and trees. Worked example of the Demo Project. Discussion on treating whole farms as single individuals. Multiple EndUses and Grouping. |
| Multiple EndUses: Extended applications | The second of two videos on the substantially upgraded Multiple Enduses feature in MateSel. You can now control traits, markers and coancestries across Enduses. Declare populations, each with one or more EndUses, and manage coancestry within and across these populations. Example applications include setting up an information nucleus/genomic reference population, new line development (including sire- and dam-lines), and setting up experimental treatments. |
| Committed Matings | Manage diversity across the full lifecycle. Force MateSel to make specified matings – usually to accommodate matings made recently. Examples in pigs, beet, aquaculture. This can handle sporadic ripening of aquaculture broadcast (also flowering in plants). Favourable simulation results. Worked example using the Demo Project, with some emphasis on management of individual coancestries. |
| Managing non-additive effects using the GMS facility | This is a generic facility for handling non-additive effects, whether the predicted merit of progeny is not simply the average of parental EBVs. The key applications relate to Genomic Mate Selection (GMS), hence the name. However, there are many other applications, including animal behaviour compatibility, control of level of selfing in plants and managing transport costs. |
| Accommodating bisexuality | Coming soon… How to represent usage constraints when an individual can be used as both a male and a female. Controlling the levels of self, duplicate and reciprocal matings. For plant breeding, and maybe some animals. But you can use this feature to trick MateSel into selecting in one sex alone. |
| Managing backup sires | Coming soon… |
| Introduction to version 7.9.12.9 | New features include: Comprehensive control of Progeny Inbreeding and Individual Coancestry, Dynamic Threshold Control, View Committed Matings in histograms, more speed etc. |