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. (2010) 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. and Scribner, K. T. (2014) Parentage and sibship inference from markers in polyploids. Molecular Ecology Resources 14: 541–553.
Wang, J. (2016) Individual identification from genetic marker data: developments and accuracy comparisons of methods. Molecular Ecology Resources 16: 163-175.
Wang, J. (2018) Estimating genotyping errors from genotype and reconstructed pedigree data. Methods in Ecology and Evolution 9: 109-120.
The program was created (version 188.8.131.52) in year 2004, and has been updated many times. The current version (184.108.40.206) 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);
- Batch run (in serial or parallel) of multiple input files.