COLONY
COLONY is a Fortran program written by Jinliang Wang . It implements a maximum likelihood method to assign sibship and parentage jointly, using individual multilocus genotypes at a number of codominant or dominant marker loci.
It can be used in estimating full- and half-sib relationships, assigning parentage, inferring mating system (polygamous/monogamous) and reproductive skew in both diploid and haplo-diploid species.
- Wang, J. (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963-1979.
- Wang, J. and Santure, A. W. (2009) Parentage and sibship inference from multilocus genotype data under polygamy. Genetics 181: 1579–1594.
- Jones, O. and Wang, J. (2009) COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources 10: 551–555.
The current version (2.0) of COLONY has the following features:
- Windows based GUI;
- Allowing both males and females to be polygamous to infer full-sibs, paternal half-sibs, and maternal half-sibs among the offspring;
- Allowing a 2-generation sample to infer parentage as well as sibships;
- Estimating population allele frequencies simultaneously with the reconstructed relationships taken into account, using Bayes’ theorem;
- Dealing with genotype data of diploid and haplo-diploid dioecious species, and diploid monoecious species with selfing;
- Using both dominant and codominant markers for relationship inference;
- Accounting for typing errors and mutations in data for relationship inference;
- Detecting typing errors and mutations in data;
- Inferring parental genotypes;
- Allowing parallel computation using multiple CPUs (cores).
Download
Colony v2.0 (Windows) (8.5 MB)
This downloads a 'zipped' file containing a Windows installer of the COLONY program for Windows. Last updated on 12/07/10.
Colony v2.0 (Macintosh) (10.3 MB)
This downloads a 'zipped' file containing an executable and user's guide of the COLONY program for Macintosh. Last updated on 12/09/09.
Colony v1.2 (Windows) (491 KB)
This downloads a 'zipped' file containing an old version of the COLONY program for Windows. The old version deals with both diploid and haploid offspring genotype data in haplo-diploid species. Last updated on 10/05/10.
Please send an email to jinliang.wang@ioz.ac.uk to register as a user after downloading these packages.