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. In the Windows version, it can also be used to simulate genotype data with a given sibship/parentage structure. Papers describing the methodology and software are listed below. 

  • 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.
  • Wang J & Scribner KT. (2014) Parentage and sibship inference from markers in polyploids. Molecular Ecology Resources 14: 541–553.

The current version (2.0.5.5) of COLONY has the following features:

  • Windows (with GUI), Linux, Mac versions;
  • Allowing both males and females to be polygamous to infer full-sibs, and paternal & maternal half-sibs among the offspring;
  • Allowing a 2-generation sample to infer parentage as well as sibships;
  • Inferring clones or duplicated individuals;
  • Estimating population allele frequencies jointly 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;
  • Allowing for autopolyploid species by converting polyploid codominant marker data to pseudo-diploid dominant marker data; 
  • 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 (Windows version only);
  • Allowing parallel computation using multiple CPUs (cores).

Download

Colony2-Windows-12-11-2014 (10.17 MB)

This downloads a 'zipped' file containing a Windows installer of the COLONY program for Windows. Last updated on 12/11/2014.

Colony2-Mac-12-11-2014 (3.86 MB)

This downloads a 'zipped' file containing a Windows installer of the COLONY program for Windows. Last updated on 12/11/2014.

Colony2-Mac-12-11-2014 (3.86 MB)

This downloads a 'zipped' file containing executables and user's guide of the COLONY program for Mac. Last updated on 12/11/2014.

Colony2-Linux-12-11-2014 (7.74 MB)

This downloads a 'zipped' file containing executables and user's guide of the COLONY program for Linux. Last updated on 12/11/2014.

ColonyUpdateHistory (2.5 KB)

This downloads a text file briefing the update history of the COLONY program for all platforms. Last updated on 12/11/2014.

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