Quantitative genetic parameters are nowadays more frequently estimated with restricted maximum likelihood using the 'animal model' than with traditional methods such as parent-offspring regressions. These methods have however rarely been evaluated using equivalent data sets. We compare heritabilities and genetic correlations from animal model and parent-offspring analyses, respectively, using d...

Many applications in genetics require haplotype reconstruction. We present a phasing program designed for large half-sibs families (as observed in plant and animals) that is robust to genotyping and map errors. We demonstrate that it is more efficient than previous versions and other programs, particularly in the presence of genotyping errors.

At the Wageningen Laboratory of Plant Breeding, a software package has been developed to query a simple structured database with variety pedigree data. The package, called Peditree, creates a tree-shaped representation of pedigree information and has several visualization and lookup options. Estimates of inbreeding coefficient within a pedigree or coefficients of coancestry among pedigrees can ...

Misspecification of relationships and of genotype data can cause problems in linkage analyses based on genome-scan data. Previous reports have focused on pairwise relationships and a simple error model. This article considers the increased information available from the joint analysis of trios of individuals, integrating this analysis with an error model that allows for the most common genotypi...

With the arrival of high throughput genotyping techniques, the detection of likely genotyping errors is becoming an increasingly important problem. In this paper we are interested in errors that violate Mendelian laws. The problem of deciding if Mendelian error exists in a pedigree is NP-complete [1]. Existing tools dedicated to this problem may offer different level of services: detect simple ...

Motivation The collection, management and visualization of clinical pedigree (family history) data is a core activity in clinical genetics centres. However, clinical pedigree datasets can be difficult to manage, as they are time consuming to capture, and can be difficult to build, manipulate and visualize graphically. Several standalone graphical pedigree editors and drawing applications exist ...

Microsatellite genetic marker data are exploited in a variety of fields, including forensics, gene mapping, kinship inference and population genetics. In all of these fields, inference can be thwarted by failure to quantify and account for data errors, and kinship inference in particular can benefit from separating errors into two distinct classes: allelic dropout and false alleles. Pedant is M...