Software
Downloads
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
Department
of Biology, University of Western Ontario, London, Ontario, N6A
5B7, Canada
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.
Genetic
differentiation consists of 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
Department
of Biology, University of Western Ontario, London, Ontario, N6A
5B7, Canada
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.
Genetic
effects consists of 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†
*Department
of Biology or †Department of Applied Mathematics, University
of Western Ontario, London, Ontario, N6A 5B7, Canada
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.
Raffle
consists of 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†
*Department
of Biology, University of Western Ontario, London, Ontario, N6A
5B7, Canada, email: bneff@uwo.ca
†Department of Zoology, University of Toronto, 25 Harbord
St, Toronto, Ontario, M5S 3G5, Canada, email: tpitcher@zoo.utoronto.ca
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).
PrDM
consists of 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§
*Department
of Biology, University of Western Ontario, London, Ontario, N6A
5B7, Canada, email: bneff@uwo.ca
†Department of Zoology, University of Toronto, 25 Harbord
St, Toronto, Ontario, M5S 3G5, Canada, email: tpitcher@zoo.utoronto.ca
§ Department of Mathematics, University of Toronto, 100 St.
George St, Toronto, Ontario M5S 3G3, Canada, email: repka@math.toronto.edu
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.
FMM
consists of 7 files:
1.
executable file (fmm.exe) [Download]
3.
data file #1 (genetics.txt) [Download]
4.
data file #2 (loci.txt) [Download]
5.
data file #3 (prior.txt) [Download]
6.
data file #4 (skew.txt) [Download]
7.
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§
*Department
of Biology, University of Western Ontario, London, Ontario, N6A
5B7, Canada, email: bneff@uwo.ca
†Department of Mathematics, University of Toronto, 100 St.
George St, Toronto, Ontario M5S 3G3, Canada, email: repka@math.toronto.edu
§ Department of Zoology, University of Toronto, 25 Harbord
St, Toronto, Ontario, M5S 3G5, Canada, email: mgross@zoo.utoronto.ca
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.
Two-Sex
Paternity consists of 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]
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