AFLPOP, version 1.1

Population assignment program for AFLP data (Amplified Fragment Length Polymorphism).

Reference : DUCHESNE, P., L. BERNATCHEZ. 2002. AFLPOP : A computer program for simulated and real population allocation based on AFLP data. Molecular Ecology Notes. 3, 380-383.

PAPA, version 2.0

Parentage allocation and simulator program assuming all potential parents have been genotyped (closed system). The allocations are based on parental pairs. Structured parental files are allowed to match many captive breeding conditions.

Reference : DUCHESNE, P., M.-H. GODBOUT, L. BERNATCHEZ.. 2002. PAPA (Package for the Analysis of Parental Allocation) : A computer program for simulated and real parental allocation. Molecular Ecology Notes. 2, 191-194.

PASOS, version 1.0

Parental allocation and simulator program to be used in open systems i.e. when some proportion of the true parents have not been collected/genotyped. designed to assess parentage, detect the proportion of uncollected parents, and calculate estimates of the probability that allocations are correct through simulations.

Reference : DUCHESNE, P., CASTRIC, T. L. BERNATCHEZ. 2005. PASOS (parental allocation of singles in open systems): A computer program for individual parental allocation with missing parents. Molecular Ecology Notes. 5: 701-704.

PERM, version1.0

PERM is a permutation program designed to detect statistical connections between grouping structures and grouping factors or correlates. PERM offers four procedures: i) Detecting a statistical link between a collection of groups and some pairwise relationship statistic such as Rxy, Mxy, half or fullsibship; ii) Comparing average values among groups for some measure or statistic; iii) Searching for connections between group structure and category e.g. population membership; iv) Detecting a statistical connection between mating couple formation and some pairwise relationship between partners such as allelic distance on an MHC locus.

Reference : DUCHESNE, P., C. ÉTIENNE, L. BERNATCHEZ. 2006. PERM: A computer program to detect structuring factors in meaningful social units. Molecular Ecology Notes. 6: 965-976.

POP-ASSIGN.XLS

Excell sheet to estimate minimal number of loci for population assignment.

Reference : BERNATCHEZ, L., P. DUCHESNE. 2000. Individual-based genotype analysis in studies of parentage and population assignment : how many loci, how many alleles ? Canadian Journal of Fisheries and Aquatic Sciences. 57:1-12.

PARENT-ASSIGN.XLS

Excell sheet to estimate minimal number of loci for parentage assignment.

Reference : BERNATCHEZ, L., P. DUCHESNE. 2000. Individual-based genotype analysis in studies of parentage and population assignment : how many loci, how many alleles ? Canadian Journal of Fisheries and Aquatic Sciences. 57:1-12.