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Unité Mixte de Recherche Inra-Univ. Bordeaux 1 "Biodiversité Gènes et Communautés" - Biogeco

Unité mixte de recherche (Inra, Univ. Bordeaux 1)Biodiversité, gènes et communautés (Biogeco) INRA_rvb150Bordeaux1

INRA Bordeaux-Aquitaine

Site de Recherches Forêt-Bois

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33612 CESTAS Cedex - FRANCE

FaMoz

A software for parentage studies

(c) Sophie Gerber, Patrick Chabrier, Antoine Kremer (contact: sophie_at_pierroton.inra.fr)

INRA, UMR BioGEco, Bordeaux-Pierroton/ INRA, Biometrics and Artificial Intelligence, Toulouse

FaMoz, a software written in the C language and in TclTk, uses likelihood calculation and simulation to perform parentage studies with codominant, dominant, cytoplasmic markers or combinations of the different types (see the diagram of FaMoz basic functioning). C codes are available on request. Any comment or feedback concerning the software is very welcome!

The TwoGener options should not be used anymore, use the software Poldisp instead.

To cite FaMoz, please use the following reference:

Gerber S., Chabrier P., Kremer A (2003) FaMoz: a software for parentage analysis using dominant, codominant and uniparentally inherited markers. Mol Ecol Notes3, 479-481.

FAMOZ (an acronym for father/mother) is a software useful in reconstructing parentage for dominant, codominant markers. It is written in C and TclTk languages and is available to be downloaded for Unix, Linux and Windows systems. Parameters and assumptions used in the calculations are few and simple. Exclusion and identity probabilities, log-likelihoods of potential father and parent or parent pair are calculated based on real or simulated data. Error rates for genotypic mistyping can be introduced. Simulations can be done to build statistical tests for parentage assignment.

See also, for description of methods implemented in FaMoz:

Gerber S, Mariette S, Streiff R, Bodénès C, Kremer A (2000) Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis. Molecular Ecology, 9, 1037-1048.

This study compares the properties of dominant markers, like AFLPs, to those of codominant multiallelic markers, like microsatellites, in reconstructing parentage. These two kind of markers were used to look for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping or not. Experimental data on 89 oak trees genotyped for 6 microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produce high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1 to 0.4 are more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO) inferred from parentage analysis with microsatellites overestimates the true GFO whereas with AFLPs, it is underestimated. As expected, dominant markers are less efficient than codominant markers to achieve this task, but can still be used with a good confidence, especially when loci are purposely selected according to their allele frequencies.

FaMoz

Diagram

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