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. 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 (2.0.5.0) 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 (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).

Download

Colony v2.0.5.0 (Windows) (12.25 MB)

This downloads a 'zipped' file containing a Windows installer of the COLONY program for Windows. Last updated on 21/05/2013.

Colony (Windows) update history (1.71 KB)

This downloads a text file briefing the update history COLONY program for Windows. Last updated on 21/05/2013.

Colony v2.0 (Macintosh) (10.31 MB)

This downloads a 'zipped' file containing an executable and user's guide of the COLONY program for Macintosh. Last updated on 12/09/2009.

Colony v1.2 (Windows) (491.39 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 10/05/2010.

Please send an email to jinliang.wang@ioz.ac.uk to register as a user after downloading these packages.