Here is a list of software packages that we realized to improve our analyses. They can be downloaded freely for non-commercial purposes:
PedVizApi is a Java Api for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data.
Please visit www.pedvizapi.org for more information and downloads.
Jenti is a tool to mine the pairwise kinship coefficient matrix of complex genealogies with multiple lines of descent and identify clusters of individuals sharing the same expected amount of relatedness through maximum-clique approach. It additionally allows for the reconstruction of sub-pedigrees suitable for genetic mapping in a systematic way (Falchi and Fuchsberger 2007).
Please visit www.jenti.org for more information and downloads.
GWAtoolbox is an R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS). Thought to be employed as a preprocessing tool in the meta-analysis of GWA data, GWAtoolbox can process multiple GWA data files in a few minutes. Output consists in an extensive list of quality statistics and graphical output, to give a comprehensive overview of the data that are going to be meta-analyzed.
Please visit GWAToolbox for more information and downloads.
LDExplorer is an R package for the memory efficient whole-genome LD-based haplotype block recognition. It is a scalable implementation of the Gabriel et al. 2002 algorithm, which is the most commonly used method for LD-based haplotype block recognition. Its low memory usage and runtime efficiency allows to process genome-wide data consisting of millions of SNPs.
Please visit LDExplorer for more information and downloads.