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. It can also be used to simulate genotype data with a given sibship/parentage structure.
- 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.
- Wang, J. (2012) Computationally efficient sibship and parentage assignment from multilocus marker data. Genetics 191: 183-194.
- Wang, J. (2013) A simulation module in the computer program colony for sibship and parentage analysis. Molecular Ecology Resources 13: 734-739.
- Wang, J. (2013) An improvement on the maximum likelihood reconstruction of pedigrees from marker data. Heredity 111: 165-174.
The current version (184.108.40.206) 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 (SNPs and SSRs) for relationship inference;
- Accounting for typing errors and mutations in data for relationship inference;
- Detecting typing errors and mutations in genotype data, and estimating mistyping rate per locus;
- Inferring parental genotypes;
- Implementing the accurate full likelihood method and the fast likelihood score method;
- Simulating multilocus genotype data with a predefined pedigree;
- Allowing parallel computation using multiple CPUs (cores).
This downloads a 'zipped' file containing a Windows installer of the COLONY program for Windows. Last updated on 30/10/2013.
This downloads a text file briefing the update history of COLONY program for Windows. Last updated on 30/10/2013.
This downloads a 'zipped' file containing an executable and user's guide of the COLONY program for Macintosh. Last updated on 12/09/2009.
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 10/05/2010.
Please send an email to email@example.com to register as a user after downloading these packages.