CBGP-softwares

INRA  Centre de Montpellier Centre de Biologie et Gestion des Populations (CBGP) Equipe / Team: Génétique et Ecologie des Populations (Gène & Pop) WWW Contact: Sylvain Piry

Logiciels de génétique des populations / Populations genetics softwares

FreeNA

Marie-Pierre Chapuis & Arnaud Estoup
FreeNA is a PC computer program which performs three major tasks on any microsatellite dataset harboring null alleles: (1) it estimates null allele frequencies for each locus and population analysed following the Expectation Maximization (EM) algorithm of Dempster, Laird, and Rubin (1977); (2) it estimates unbiased FST (Weir 1996) following the ENA method described in Chapuis and Estoup (2007); (3) it computes a genotype dataset corrected for null alleles following the INA method described in Chapuis and Estoup (2007), which may be used to calculate the Cavalli-Sforza and Edwards’ (1967) genetic distance. All methods used in this program are tested and discussed in Chapuis and Estoup (2007).

May 2007, 27th. FreeNA update: the new version enables the computation of 95% confidence intervals for pairwise Fst values by bootstrap procedure.

Reference

Chapuis, M.-P. and Estoup, A. (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24(3): 621-631.

Download executable for windows
README file [also see note below]

Important note: Because the INA corrected datafile makes the unrealistic assumption of a single null allele state common to all populations, we strongly discourage the use of this file for all population genetics analyses but the computation of the Cavalli-Sforza and Edwards’(1967) genetic distance, unless carefully testing the performance of such a file for the concerned analysis.

GeneClass2

GeneClass2 est un logiciel permettant de choisir ou d'exclure des populations comme étant l'origine d'individus à partir de génotypes multilocus (affectation et détection de migrants). Cette nouvelle version a été entièrement réécrite, elle inclue les fonctionnalités de pop100gene.

Voir la page d'installation.
Télécharger l'installateur de la version bilingue anglais/français en français pour Windows®
Télécharger la version bilingue anglais/français pour Linux® (format RPM ou fichier .tar.gz)
S'enregistrer pour être tenu informé des nouvelles versions ou des nouveaux logiciels
Voir l'aide en ligne (en Français) [existe aussi en PDF]

Référence

Piry S, Alapetite A, Cornuet, J.-M., Paetkau D, Baudouin, L., Estoup, A. (2004) GeneClass2: A Software for Genetic Assignment and First-Generation Migrant Detection. Journal of Heredity 95:536-539.

Historique et bugs

• Attention, un bug était présent dans la version d'août (08/2003), qui génère un classement erronné si on utilise les distance avec le rééchantillonnage.
• Version de février 2004 (2.0.b). La lecture est fichiers textes (ex. genepop) est améliorée.
• Version de juin 2004 (2.0.d) : encore des corrections du bug "Invalid floating point error" dans le calcul de distances qui subsistait parfois avec la 2.0.c. Merci aux testeurs !
• Version de juillet 2004 (2.0.e) : correction du plantage au lancement sur certaines machines.
• Version de décembre 2004 (2.0.f) : Correction du plantage au lancement avec Windows XP-SP2, correction de la sélection des locus.
• Version de janvier 2005 (2.0.g) : Correction d'un bug dans le traitement des données manquantes en cas de désélection de locus. Merci à Alain Frantz qui l'a découvert.

 

GeneClass2 is a program employing multilocus genotypes to select or exclude populations as origins of individuals (Assignment and Migrants Detection). This is a completely rewritten new version that includes pop100gene features.

See the installation page.
Download setup file of bilingual english/french version in english for Windows™
Download bilingual english/french version for Linux® (format RPM or .tar.gz file.)
Register if you want to be informed of new releases or new softwares.
See the online helpfile (in English) [also exists in PDF]

Reference

Piry S, Alapetite A, Cornuet, J.-M., Paetkau D, Baudouin, L., Estoup, A. (2004) GeneClass2: A Software for Genetic Assignment and First-Generation Migrant Detection. Journal of Heredity 95:536-539.

History and bugs

• Warning: A bug has been discovered in the august version (08/2003) leading to an erroneous assignment while using distances with resampling.
• Feb. 2004 release (2.0.b): Text files (eg. genepop) parsing improved.
• June 2004 release (2.0.d): more correction of the "Invalid floating point error" bug while computing distances, sometimes still occuring with 2.0.c version. Thanks to the testers !
• July 2004 release (2.0.e): correction of the crash when starting on some machines.
• December 2004 release (2.0.f): correction of the crash at start under Windows XP-SP2, and correction of the loci selection.
• January 2005 (2.0.g): Correction of a bug involving missing data treatment when some loci are unselected. Thanks to Alain Frantz who discovered it.

GeneClass (Ancienne version / Old version)

A program employing multilocus genotypes to select or exclude populations as origins of individuals.

Bottleneck

Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies.

JMS-v1

JMS-v1 is a computer program for a simulation-based evaluation of the diagnostic status of juxtaposed microsatellite systems.

Look at the README file (exists also in pdf format).
Download the program and other files (PC only).

Cours / Courses

Les documents relatifs à l'école chercheurs MICROSATELLITES qui s'est tenue à La Grande-Motte (Hérault) du 27 au 31 mars 2000.

The transparencies concerning the MICROSATELLITES workshop, held in La Grande-Motte (Hérault) from march 27th to 31th 2000.

Apis Project

Additional informations (coloured version of figure 7) for an article in Evolution.

Additional informations (tables of allelic frequencies at 8 microsatellites loci and 10 populations) in Acrobat pdf format for an article in Apidologie.

Additional informations (tables of allelic frequencies at 8 microsatellites loci and 12 populations) in Acrobat pdf format for an article in Molecular Ecology.

Additional informations (distribution of COI-COII mitotypes at 82 locations) in Acrobat pdf format for an article in Heredity.

Additional informations (raw data: genotypes and fratery distributions) in Acrobat pdf format for an article in Animal Behaviour.