dr hab. Chybicki Igor JerzySoftware
RSPMi 1.0 download
The software designed for the estimation of seed and pollen migration in plants using genotypic data. The program requires a sample of individuals from a network of populations, genotyped at a number of nuclear (codominant) markers (e.g. microsatellites or SNPs). RSPMi yields Bayesian estimates of migration rates separately for seeds and pollen, specifically for each population pair. In addition, the program yields the estimates of before-migration differentiation (Fst-like) parameters, and individual inbreeding coefficients. The latter may be optionally estimated simultaneously with allelic dropout rates, accounting for increased homozygosity related to technical issues rather than identity by descent. The program is related to a paper by Igor J. Chybicki and Juan J. Robledo-Arnuncio "Spatially explicit estimation of recent migration rates in plants using genotypic data" accepted for publication in Genetics.
quedo download
the software designed for quantifying ecological determinants of outcrossing rates in plant populations. quedo implements the hierarchical Bayesian approach for modeling the single- or multi-locus outcrossing rates using a non-linear regression model. Model selection is performed using the Reversible-Jump Markov Chain Monte Carlo. The approach requires data on genotypes of progeny grouped into maternal families as well as potential explanatory variables for outcrossing, such as individual traits (dbh, distance to nearest male, etc.) and population characteristics (age, size, density, pollinator abundance or diversity, etc.). The method accounts for genotyping errors and genetic structure among populations.
NMπ download
New version 2.0: new Bayesian procedures to minimize the risk of false positives among determinants of reproductive success
(the manuscript on NMπ 2.0 accepted for publication in Molecular Ecology Resources)
The package contains a short video showing how to set up the Bayesian analysis (Hierarchical Neighborhood Model) on a personal computer with limited computational capacity (using Windows-based interface).
the software designed for the estimation of plant mating systems and seed and pollen dispersal kernels. NMπ is a re-implementation of the NM+ program and provides new features such as support for multi-core processors, an explicit treatment of dioecy, the possibility of incorporating uniparentally cytoplasmic markers, the possibility of assessing assortative mating due to phenotypic similarity and inference about offspring genealogies. The probability model of parentage (the neighborhood model) accounts for missing data and genotyping errors, which can be estimated along with regular parameters of the mating system. The program has virtually no restrictions with respect to the number of individuals, markers, or phenotypic characters. A console version of NMπ can be run under a wide variety of operating systems, including Windows, Linux, or Mac OS. For Windows users, a graphical user interface is provided to facilitate operating the software.
sgssimul.f95 download
The Fortran code (and the Windows executable file) of a simulation program generating data through a forward-time isolation-by-distance process occurring in a single isolated plant population. The code compiles easily under the GNU Fortran compiler (GCC ver. 5.2.0) and runs smoothly under both Windows and Linux. sgssimul was used in Chybicki et al. (2016) Relative strength of the fine-scale spatial genetic structure in paternally vs. biparentally inherited DNA in a dioecious plant depends on both sex proportions and pollen-to-seed dispersal ratio. Heredity 117:449-459.
CEMBRA download
(Cembra is now replaced by quedo)
The software was designed primarily to verify the association between outcrossing rates and nominal or continuous predictors. The Bayesian method is described in the TGG paper. In the updated version, cembra allows unbiased estimation of biparental inbreeding, defined as the effective selfing rate (Chybicki, submitted).
INEST 2.3 download
(last update: April 24, 2024 - bug fixes regarding problems with bottleneck testing for a huge number of markers)
The newest, completely re-implemented version of the software. Here, the Bayesian approach is available together with procedures for model comparison. This can be helpful to determine if inbreeding is present in the data (see Chybicki et al. 2011, the Taxus paper). If coordinates are available, the spatial genetic structure can be also assessed. For this purpose 5 genetic similarity indices are available (Nason, Moran, Ritland, Queller-Goodnight, and semivariance). Additionally, the permutation test for heterozygosity excess (HW test) can be performed. Since version 2.1, the test for the bottleneck is implemented. This procedure follows exactly the algorithm in Luikart and Cornuet (1996) and, under the SMM or TPM model of mutation, provides better p-values associated with the Wilcoxon test compared to the BOTTLENECK software. Since version 2.2, INEST provides new functionality in terms of empirical Bayes estimates of observed and expected heterozygosity corrected for null alleles.
INEst estimates frequencies of null alleles at SSR loci within a population. However, its unique feature is to take into account the possibility of inbreeding within a population during the estimation of null allele frequencies. It is well known, that both inbreeding and null alleles can cause an excess of homozygotes within a population. So the best strategy is to estimate both inbreeding and null allele frequencies simultaneously. That is why INEst may outperform other available packages (see here).
NM2F download
New version: selection gradients robust to overdispersion in male fecundity!!!
The Bayesian implementation of the neighborhood model (Adams and Birkes 1991) that allows inferring mating patterns (using half-sib families and candidate fathers) at the individual level, including pollen immigration, self-fertilization, pollen dispersal, individual male fecundity, and genetic structure of immigrant pollen. The new version estimates selection gradients using the approach robust to overdispersion in male fecundities, as described in our recent MER paper.
The older version of NM2F, used in the AoB paper, is available from the author upon request.
MSF 1.01 download
The Bayesian implementation of the mixed mating model with some useful additions, like a model for typing errors, a possibility for family contamination (a presence of progeny individuals which are not related to the putative mother plant), and a model for pollen pool structure (the F-model). Some methods were described in the Journal of Heredity (Chybicki 2013), Annals of Botany (Chybicki and Burczyk 2013), and Apidologie (Oleksa et al. 2013).
I4A download
The software used in the Taxus baccata paper (Heredity 107:589) in order to estimate inbreeding levels based on dominant markers.
