jenti


mario falchi1and christian fuchsberger2

1Twin Research & Genetic Epidemiology Unit, Kings College London, London
2Institute of Genetic Medicine, European Academy, Bolzano, Italy


Description Documentation Tutorial Download Forum m.falchi@imperial.ac.uk

Summary
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).

Why Jenti?
When dealing with complex genealogies, it is sometimes useful to extract the sub-sample of the most related/unrelated individuals, or to split the whole genealogy in homogeneous sub-samples. Systematic clustering is unfeasible without an appropriate computational tool, because of the massive number of possible configurations.

Features
Jenti explores the kinship relationships among all the individuals and identify the sub-group(s) configuration which maximizes the overall number of extracted pairwise relationships.Through a user-friendly graphical interface, the user is assisted step-by-step in the in the selection process, from the exploration and cleaning of the whole genealogical data to the manual or semi-automatic clustering of individuals in homogeneous sub-groups.

System requirements
Java VM 5.0/1.5 or higher Get Java
(To check Java version, type "java -version")
For 2.5D Visualization (additional): Java 3D v1.4.2 or higher and up-to-date graphic card drivers.

Reference
Jenti: an efficient tool for mining complex inbred genealogies.
Mario Falchi and Christian Fuchsberger
Bioinformatics 2008 24: 724-726.

In Use
Bellenguez C, Ober C, Bourgain C.
A multiple splitting approach to linkage analysis in large pedigrees identifies a linkage to asthma on chromosome 12.
Genet Epidemiol. 2008 Oct 6.

Acknowledgement
Lukas Forer for the work on the pedvizapi, Clemens Egger for technical support.

Freeware License
Copyright 2007 by Mario Falchi. All rights reserved.
Redistribution and use in binary forms, are permitted provided that the following conditionis met:
Redistributions in binary form must reproduce the above copyrightnotice, this list of conditions and the following disclaimer in thedocumentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' ANDANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THEIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSEARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLEFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIALDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODSOR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICTLIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAYOUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OFSUCH DAMAGE.