- Windows Executable
- Executable for Linux on Sun processor
- Executable for Linux on Intel processor
- Documentation (Readme file)
- Example infile

PATRI (PaTeRnity Inference) is a program for paternity analysis of genetic
data. The program requires genotypic, diploid data from one or more loci from
mother-offspring pairs and from potential fathers. Typical data might include
microsatellite markers, Restriction Fragment Length Polymorphisms (RFLPs) or
Single Nucleotide Polymorphisms (SNPs). Given such genotypic data, PATRI can
calculate posterior probabilities of paternity for all sampled offspring. When
behavioral or ecological information can be used to divide the sampled males
into different groups, PATRI can perform maximum likelihood analyses of
hypotheses regarding the relative reproductive success of those groups. The
underlying statistical methodology was described in Nielsen,R., Mattila,D.K.,
Clapham,P.J. and Palsbøll,P.J. 2001. Statistical Approaches to Paternity
Analysis in Natural Populations and Applications to the North Atlantic
Humpback Whale. *Genetics *157:1673-1682.

For all genotypes, PATRI can estimate the posterior probability that a
particular male has sired a particular offspring, assuming a uniform prior
among all males in the population. The male population size (*N*) can
either be specified by the user as a fixed value, or uncertainty regarding
*N* can be modeled using a uniform or Gaussian prior. Using a uniform
prior corresponds to assuming no prior information regarding the male
population size, except that an upper bound can be specified. PATRI can also
produce a maximum likelihood estimate of *N* based solely on the
parent-offspring genotypic data. The estimation of *N* assumes equal
fecundity and unbiased sampling of males.

If sampled males can be divided into groups based on behavioral or
ecological information, PATRI can be used to evaluate hypotheses regarding the
relative reproductive success of these groups. For *k* groups the user
starts with a full model containing *k*-1 parameters, *a*_{2}, *a*_{3},\u2026,*a _{k}*, where