The Fortran code of simulation program generating data through a forward-time isolation-by-distance process occuring in a single isolated plant population. The code compiles easily under GNU Fortran (4.9.2) and runs smoothly under both Windows and Linux (The code will be made available once the manuscript, which describes the methods and results, has been accepted for publication).
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.
(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 2.0 download
I'm pleased to announce that the JoH paper reached 100 citations (based on Web of Science Core Collection)...
(last update: January 30, 2015)
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.
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).
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.)
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).
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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