COLONY

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.
• Wang, J. (2012) Computationally efficient sibship and parentage assignment from multilocus marker data. Genetics 191: 183-194.

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 (SNPs and SSRs) for relationship inference;
• Accounting for typing errors and mutations in data for relationship inference;
• Detecting typing errors and mutations in data;
• Inferring parental genotypes;
• Implementing the accurate full likelihood method and the fast likelihood score method;
• Allowing parallel computation using multiple CPUs (cores).