CBGP-softwares
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Centre de Biologie et Gestion des Populations (CBGP) WWW Contact: Sylvain Piry |
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Centre de Biologie et Gestion des Populations (CBGP) WWW Contact: Sylvain Piry |
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Logiciels de génétique des populations / Populations
genetics softwares
PIFs
PIFs (acronym of Pool_Ind_Freq_SNP.xls) is an excel encoded application (compatible with OpenOffice Calc) that includes various graphical and numerical outputs which allow NGS practitioners to assessing and comparing the precision in allele frequency estimation for both pool and diploid individual SNP data under various sampling, coverage and experimental error designs. Details about the underlying assumptions and mathematical derivations are provided in Gautier et al. (2013).
References
- Gautier M., Foucaud J., Gharbi K., Cezard T., Galan M., Loiseau A., Thomson M., Pudlo P., Kerdelhue C. and Estoup A. (2013) Estimation of population allele frequencies from next-generation sequencing data: pooled versus individual genotyping. Molecular Ecology in revision.
README file
poolne_estim
poolne_estim is a program implementing a Markov Chain Monte Carlo algorithm to sample the posterior distribution of the different parameters underlying the Bayesian hierarchical model described in Gautier et al. (2013). It is primarily aimed at estimating in Pool-Seq experiment the effective diploid size of pools/replicates (e.g. identified by molecular barcodes) from SNP allele count data. Note that each pool (or replicate) are assumed to originate from the same population.
- Gautier M., Foucaud J., Gharbi K., Cezard T., Galan M., Loiseau A., Thomson M., Pudlo P., Kerdelhue C. and Estoup A. (2013) Estimation of population allele frequencies from next-generation sequencing data: pooled versus individual genotyping. Molecular Ecology in revision.
Download poolne_estim 1.0 linux executable
kim_tree
kim_tree is a program implementing a Markov Chain Monte Carlo algorithm to sample the posterior distribution of the different parameters underlying the Bayesian hierarchical model described in Gautier and Vitalis (2013). This method is primarily aimed at estimating divergence times on a diffusion time scale from large single-nucleotide polymorphism (SNP) data sets, conditionally on a population history that is represented as a tree. Assessing model fit using the deviance information criterion (DIC) also proved efficient for retrieving the correct tree topology among a set of competing histories.
- Gautier M. and Vitalis R. (2013) Inferring population histories using genome-wide allele frequency data. Molecular Biology and Evolution 30(3): 654-668.
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 calculates the Cavalli-Sforza and Edwards (1967) genetic distance following the INA method described in Chapuis and Estoup (2007). All methods used in this program are tested and discussed in Chapuis and Estoup (2007).
November 2009, 16th. FreeNA update: the new version replaces the computation of a genotype dataset corrected for null alleles following the INA method and to be used to calculate the Cavalli-Sforza and Edwards (1967) genetic distance by a direct estimation of pairwise values for the Cavalli-Sforza and Edwards (1967) genetic distance following the INA method. This includes the computation of 95% confidence intervals computed by bootstrap procedure. This is because the INA corrected datafile makes the unrealistic assumption of a single null allele state common to all populations. As a result, the use of such a file is strongly discouraged for all population genetics analyses unless carefully testing the performance of such a file for the concerned analysis (see reference Chapuis et al. 2008). Computer simulations showed that the INA correction method provided slightly biased estimates of Cavalli-Sforza and Edwards (1967) genetic distance, but give better estimates than those obtained without correction (Chapuis and Estoup 2007).
Improvements also include removal (i) of a bug in reading genotype datasets with large numbers of loci (although the error was obvious with identical estimates for loci >50, be sure to replace your existing version) and (ii) of limit constraints in numbers of loci and populations that should make FreeNA running for larger datasets.
- Chapuis, M.-P. and Estoup, A. (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24(3): 621-631.
- Chapuis M.-P., M. Lecoq, Y. Michalakis, A. Loiseau, G. A. Sword, S. Piry, and A. Estoup. (2008) Do outbreaks affect genetic population structure? A worldwide survey in Locusta migratoria, a pest plagued by microsatellite null alleles. Molecular Ecology 17(16): 3640-3653.
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.
S'enregistrer pour être tenu informé des nouvelles versions ou des nouveaux logiciels
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.
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.
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.
CBGP/softwares/
- 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.
GeneClass (Ancienne version / Old version)
A program employing multilocus genotypes to select or exclude populations as origins of individuals.
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.
Cours / Courses
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Apis
Project
Additional informations (coloured version of figure 7) for an article in Evolution.
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