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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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COLONY: a program for parentage and sibship inference from multilocus genotype data.

Owen R Jones¹, Jinliang Wang

¹Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.

Molecular Ecology Resources

|May 14, 2011

Summary

This summary is machine-generated.

We introduce colony, a flexible software for inferring genetic relationships in wild populations. It uses full-pedigree likelihood methods to simultaneously determine parentage and sibship, accommodating various species and marker types.

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Area of Science:

Population Genetics
Bioinformatics
Computational Biology

Background:

Pedigrees are crucial for understanding genealogical relationships in research.
Molecular markers enable pedigree inference in wild species where direct observation is challenging.
Existing pedigree analysis software often lacks flexibility in handling diverse species, marker types, and data complexities like genotyping errors.

Purpose of the Study:

To introduce colony, a novel computer program designed for comprehensive pedigree analysis.
To implement full-pedigree likelihood methods for simultaneous inference of parentage and sibship.
To provide a flexible tool that accommodates various biological and data conditions.

Main Methods:

Utilizes full-pedigree likelihood methods for analyzing multilocus genotype data.
Accommodates both diploid and haplodiploid species.
Supports dominant and codominant markers, and can estimate genotyping errors.

Main Results:

The colony program successfully infers parentage and sibship simultaneously.
Demonstrates flexibility in handling diverse species (monoecious and dioecious) and marker types.
Incorporates the capability to manage and estimate genotyping errors, enhancing accuracy.

Conclusions:

colony offers a significant advancement in pedigree analysis software due to its flexibility and comprehensive approach.
The program is suitable for a wide range of applications in population genetics and evolutionary biology.
Available in user-friendly Windows and R-based Macintosh versions for broad accessibility.