Genetic Differentiation Software
A program to compare genetic differentiation statistics across loci using resampling of individuals and loci
Bryan D. Neff and Bonnie A. Fraser
Description
This program statistically compares FST or G'ST estiamtes from two locus-types (e.g. MHC versus microsatellites) by resampling individuals within pairs of populations and/or loci to generate confidence intervals in the genetic differentiation estimates.
Download (4 files)
1. executable file (Neff&Fraser_Fst.exe) [Download]
2. data file 1 (MHCdata.txt) [Download]
3. data file 2 (MICdata.txt) [Download]
4. help file (readme.pdf) [Download]
Genetic Effects Software
MHC class IIB alleles contribute to both additive and non-additive genetic effects on survival in Chinook salmon
Trevor E. Pitcher and Bryan D. Neff
Description
This program partitions variance in familial data, such as offspring body sizes or survivorship, to both additive and non-additive genetic effects at a candidate locus.
Download (3 files)
1. executable file (Neff&Pitcher_GA.exe) [Download]
2. data file (gadata.txt) [Download]
3. help file (readme.pdf) [Download]
Raffle Software
Mechanisms of sperm competition: testing the fair raffle
Bryan D. Neff and Lindi M. Wahl
Description
This program uses the maximum likelihood methods developed by Neff and Wahl (2004) to examine the mechanisms of sperm competition. The model calculates the relative competitiveness of two males’ sperm ("loadings" = r) as well as the economy of scale (non-linear returns to sperm number = t) and compares these to a defined null hypothesis for r and t - e.g., for the fair raffle r = 1 and t = 1.
Download (3 files)
1. executable file (Neff&Wahl_Raffle.exe) [Download]
2. data file (raffledata.txt) [Download]
3. help file (readme.pdf) [Download]
PrDM Software
Assessing the statistical power of genetic analyses to detect multiple mating in fish
Bryan D. Neff and Trevor E. Pitcher
Description
This program calculates the probability of detecting a multiple mating (fertilization) in a sample of offspring. The model assumes single-sex multiple mating (i.e., polygyny or polyandry) and therefore all offspring in a brood are either full-sibs or half-sibs. The criterion used to detect the multiple mating is three or more paternal alleles in the set offspring. The program is written in C++ for PC-type computers and is an executable file (PrDM.exe). It is run by double clicking the icon or using the ‘Run’ command line (see the help file for more details).
Download (3 files)
1. executable file (PrDM.exe) [Download]
2. data file (MMdata.txt) [Download]
3. help file (readme.doc) [Download]
FMM Software
A Bayesian model for assessing the frequency of multiple mating in nature
Bryan D. Neff, Trevor E. Pitcher, and Joe Repka
Description
This program calculates the frequency of multiple mating (fmm) in a population based on a sample of nests. It places the algorithm developed by Neff and Pitcher for calculating the probability of detecting a multiple mating (PrDM) into a Bayesian framework. The program outputs the probability distribution associated with each fmm from 0 to 100% in increments of 1%. From the distribution the expected fmm is calculated as well as any desired confidence interval.The model assumes single-sex multiple mating (i.e., polygyny or polyandry). The criterion used to detect the multiple mating is three or more paternal alleles in the set offspring. The program is written in C++ for PC-type computers and is an executable file (fmm.exe). It is run by double clicking the icon or using the ‘Run’ command line. See the help file for more details.
Download (6 files)
1. executable file (fmm.exe) [Download]
2. data file #1 (genetics.txt) [Download]
3. data file #2 (loci.txt) [Download]
4. data file #3 (prior.txt) [Download]
5. data file #4 (skew.txt) [Download]
6. help file (readme.pdf) [Download]
Two-Sex Paternity Software
Parentage analysis with incomplete sampling of candidate parents and offspring
Bryan D. Neff, Joe Repka, and Mart R. Gross
Description
This program calculates the paternity (or maternity) of a putative parent to a sample of next generation individuals (NGIs) following the equations outlined in Neff, Repka and Gross (2000a,b) and Neff (2001). The program is run by double clicking the "2sexpat.exe" file (from windows explorer, for example). The program requires three input files outlined below, and outputs the most-likely paternity, the expected paternity and the 95% confidence interval in the paternity estimate.
Download (5 files)
1. executable file (2sexpat.exe) [Download]
2. data file #1 (alledata.txt) [Download]
3. data file #2 (genedata.txt) [Download]
4. data file #3 (priordis.txt) [Download]
5. help file (readme.doc) [Download]