A novel web-based tool PedWiz that pipelines the informatics process for pedigree data is introduced. PedWiz is designed to assist researchers in the analysis of pedigree data. It provides a convenient tool for pedigree informatics: descriptive statistics, relative pairs, genetic similarity coefficients, the variance-covariance matrix for three estimated coefficients of allele identical-by-desc...

Pedigree polytopes are extensions of the classical Symmetric Traveling Salesman Problem polytopes whose graphs (1-skeletons) contain the TSP polytope graphs as spanning subgraphs. While deciding adjacency of vertices in TSP polytopes is coNP-complete, Arthanari has given a combinatorial (polynomially decidable) characterization of adjacency in Pedigree polytopes. Based on this characterization,...

The objective of this study was to test the performance of a recently proposed methodology for the estimation of realized effective size (N(e)) based on individual increase in inbreeding (DeltaF(i)) on several real pedigrees: (a) an experimental mice population; (b) a closed pedigree of fighting bulls; (c) the Spanish Purebred (SPB, Andalusian) horse pedigree; (d) the Carthusian strain of SPB p...

The classical polytope associated with the symmetric traveling salesman problem (STSP) is usually studied as embedded in the standard subtour elimination polytope. Several classes of facet defining inequalities of the STSP polytope are used in practical enumeration algorithms. In this paper we consider the basic objects called pedigrees which are in 1-1 correspondence with the tours. The convex...

Genomic selection is widely used in dairy cattle breeding, but still, single-step models are rarely national evaluations. New computing methods have allowed the utilization of very large genomic data sets. However, an unsolved model problem how to build genomic- (G) and pedigree- (A22) relationship matrices that satisfy theoretical assumptions about same scale equal base populations. Incompatib...

In this paper, a linear-time algorithm, which is optimal, is presented to solve the haplotype inference problem for pedigree data when there are no recombinations and the pedigree has no mating loops. The approach is based on the use of graphs to capture SNP, Mendelian and parity constraints of the given pedigree.

Several studies over the last 15 yr have estimated the magnitude of cytoplasmic inheritance of production and type traits in dairy cattle. Pedigree information can be used to assign maternal lineages, and the between-maternal lineage variance is then assumed to be an estimate of cytoplasmic inheritance. Two potential sources of bias and reduction of the power of estimation of cytoplasmic inheri...

As genetic maps become denser, the effect of laboratory typing errors becomes more serious. We review a general method for detecting errors in pedigree genotyping data that is a variant of the likelihood-ratio test statistic. It pinpoints individuals and loci with relatively unlikely genotypes. Power and significance studies using Monte Carlo methods are shown by using simulated data with pedig...

Pedigree MatchMaker is an RFID panel reader system that collects sheep movements to and from watering points over a 2 week period to identify pedigree. While this system was primarily developed to identify the pedigree of lambs, it may also provide information relating to lamb and ewe behaviour traits which influence sheep performance. Traits were calculated from the Pedigree MatchMaker data to...