dr hab. Chybicki Igor JerzySoftware

NMπ  download

 

the software designed for estimation of plant mating system 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, 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 a number of individuals, markers or phenotypic characters. A console version of NMp 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 occuring 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 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.

 


 

NM+ (ver. 1.1)  download

 

NM+ is a computer software designed to make inferences on plant gene dispersal and mating patterns via modelling parentage probabilities based on a spatially explicit parentage model called neighbourhood model. Therefore, NM+ requires a sample of mapped and genotyped candidate parents and offspring, however offspring may optionally be assigned to single maternal parents (forming so-called half-sib progeny arrays). Using the maximum likelihood approach, NM+ estimates a number of parameters, including self-fertilization rate, immigration rates from outside of a defined study site, parameters of pollen (and/or seed) dispersal kernels (exponential-power, Weibull, geometric or 2Dt) and selection gradients relating covariates (phenotypic traits) with male (and/or female) reproductive success. By default NM+ is for studying plant populations; however, it can be used for any organism as long as data requirements and model assumptions are met. NM+ runs under Windows, but it can be launched under Linux using WINE emulator.

 

The version 1.1 assumes a possibility of random typing errors instead of null alleles. 'Typing errors' option inherited the interface of 'null alleles', so it will be relatively easy to set-up the analysis following the suggestions in the manual.

 


 

CEMBRA download

 

(Last update: 16.12.2014)

 

The software designed primarily to verify the association between outcrossing rates and nominal or continuous predictors. The Bayesian method is described in TGG paper. In the updated version, cembra allows unbiased estimation of biparental inbreeding, defined as the effective selfing rate (Chybicki, submitted).

 


INEST 2.2 download (200+ WoS citations)

 

(last update: September 14, 2017 - porting to new programming environment; added new functionality: Bayesian estimates of observed and expected heterozygosities per locus corrected for null alleles)

 

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, 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 bottleneck is implemented. This procedure follows exactly the algorithm in Luikart and Cornuet (1996) and, under 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 a 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 apopulation. However, its unique feature is to take into account a possibility of inbreeding within a population during estimation null allele frequencies. It is well known, that both inbreeding and null alleles can cause 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).

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Older version (not developed further):

INEst (ver. 1.1) download

 

(Please note that the INEST 1.1 package provides an uncomplete manual, so that the access to some functions is somewhat limited.)

 


NM2F  download

 

The Bayesian implementation of the neighbourhood model (Adams and Birkes 1991), that allows to infer about mating patterns (using half-sib families and candidate fathers) at individual level, including pollen immigration, self-fertilisation, intra- vs. inter-specific mating preferences, pollen dispersal, individual male fecundity and genetic structure of immigrant pollen. NM2F was used in the AoB paper.

 


MSF 1.01  download

 

The Bayesian implementation of the mixed mating model with some useful additions, like model for typing errors, a possibility for family contamination (a presence of progeny individuals which are not related with the putative mother plant) and a model for pollen pool structure (the F-model). Some methods were described in 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.

 

 


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