PedigreeQuery 20080410 – Drawing Pedigrees step-by-step

PedigreeQuery 20080410

:: DESCRIPTION

PedigreeQuery is a program for working with large pedigrees. Some times it is required to get chart only of some shapes of such pedigrees. PedigreeQuery was made for drawing shapes of pedigrees using step-by-step algorithm. The drawing unit is a nuclear family. New nuclear family is added to pictured shape of pedigree on each step. Enlargement of shape is making by pointing on person who is already in shape and we will called him pointer. If there are offspring or parents of the pointer which are not yet in the shape they will added to it. Step-by-step algorithm allows to draw any shape of pedigrees or whole pedigrees.

::DEVELOPER

Laboratory of the Methods of Genetic Analysis , Institute of Cytology and Genetics, Novosibirsk, Russia.

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux
Java

:: DOWNLOAD

PedigreeQuery

:: MORE INFORMATION

Citation:

Genetika. 2004 Oct;40(10):1425-8.
[An algorithm of step-by-step pedigree drawing].
[Article in Russian]
Kirichenko AV.

PEDIGREE-EXPLORER 2.0 – Explore Pedigree

PEDIGREE-EXPLORER 2.0

:: DESCRIPTION

PEDIGREE-EXPLORER is a program package with a focus on genetic-epidemiological questions as they typically occur prior to linkage analysis.

::DEVELOPER

Michael Steffens , Institute for Medical Biometry, Informatics and Epidemiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

PEDIGREE-EXPLORER

:: MORE INFORMATION

PEDSYS 2.0 – Database System for Management of Genetic, Pedigree and Demographic data

PEDSYS 2.0

:: DESCRIPTION

PEDSYS is a database system developed as a specialized tool for management of genetic, pedigree and demographic data. It has been designed principally for use with pedigree analysis of either human or non-human subjects. The system supports integrated collection, management and analysis of constantly evolving data sets by investigators in several different laboratories. Although some of the programs are specialized, many are general enough to be used effectively with data of any sort.

::DEVELOPER

Texas Biomed’s Department of Genetics

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows/MacOsX

:: DOWNLOAD

PEDSYS

:: MORE INFORMATION

ExomePicks 20100412 – Suggest Individuals to be Sequenced in a Large Pedigree

ExomePicks 20100412

:: DESCRIPTION

ExomePicks is a program that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections.

::DEVELOPER

Christian Fuchsberger

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux/Windows/MacOsX
C++ Compiler

:: DOWNLOAD

ExomePicks

:: MORE INFORMATION

EPDT 1.0 – Extended Pedigree Disequilibrium Test

EPDT 1.0

:: DESCRIPTION

EPDT (Extended Pedigree Disequilibrium Test) is a major advancement in detecting linkage/disequilibrium signals between genetic markers and disease loci, particularly if only one or a few large pedigrees are available. The strategy differs from conventional approaches that require at least a moderate number of families to attain adequate statistical power. The proposed testing procedure is advantageous in that it provides high statistical power coupled with reduced sample collection. Furthermore, the proposed method avoids problems such as potential population stratification and genetic heterogeneity, and is robust with respect to misspecification of phenotype.

::DEVELOPER

Chun-Liang Chen, Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

EPDT

:: MORE INFORMATION

Citation

H.C. Yang, C.L. Chen, and C.S.J. Fann (2004).
A pedigree-based disequilibrium test for a single extended pedigree

Endog 4.8 – Analyse Pedigree Information

Endog 4.8

:: DESCRIPTION

ENDOG‘s Primary functions are the computation of the individual inbreeding (F) (Wright, 1931) and the average relatedness (AR) (Gutiérrez et al., 2003; Goyache et al., 2003) coefficients. Additionally, users can compute with ENDOG useful parameters in population genetics such as that described for Biochard et al. (1997) for the number of ancestors explaining genetic variability or those proposed by Robertson (1953) and Vassallo et al. (1996) for the genetic importance of the herds. ENDOG also can compute F statistics (Wright, 1978) from genealogical information following Caballero and Toro (2000; 2002). Moreover, the present version of ENDOG calculates effective population size following different methodologies including regression approaches and particularly the recently proposed realized effective population size from individual increase in inbreeding (Gutiérrez et al., 2008), modified to account for avoidance of self-fertilization (Gutiérrez et al., 2009).

::DEVELOPER

Juan Pablo Gutiérrez García

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Endog

:: MORE INFORMATION

Citation

A note on ENDOG: a computer program for analysing pedigree information.
Gutiérrez JP, Goyache F.
J Anim Breed Genet. 2005 Jun;122(3):172-6.

Prest-plus 4.09 – Detection of Misspecified Relationships in Pedigrees

Prest-plus 4.09

:: DESCRIPTION

Prest-plus (Pedigree RElationship Statistical Test) is a software packages for detection of pedigree errors, cryptic relatedness and relationship mispecification in GWAS or linkage data. Using an optimized MLE estimator for IBD probabilities, prest-plus computes accurate estimates for IBD0/1/2 using any number and combination of SNP or microsatellite marker data. It can work as efficiently and accurately with a microsatellite linkage panel or SNP data from a GWAS study.

::DEVELOPER

Apostolos Dimitromanolakis and Lei Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
C Compier

:: DOWNLOAD

Prest-plus

:: MORE INFORMATION

Citation

Hum Hered. 2002;54(2):99-110.
Enhanced pedigree error detection.
Sun L, Wilder K, McPeek MS.

ROADTRIPS 1.2 – Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure

ROADTRIPS 1.2

:: DESCRIPTION

ROADTRIPS is a C program that performs single-SNP, case-control association testing in samples with partially or completely unknown population and pedigree structure.ROADTRIPS uses an empirical covariance matrix calculated from genomewide SNP data to correct for unknown population and pedigree structure, while maintaining high power by taking advantage of known pedigree information when it is available. The program is applicable to association studies with completely general combinations of related and unrelated individuals. Analysis can be performed genomewide (currently just for autosomes).

::DEVELOPER

Timothy Thornton and Mary Sara McPeek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
C Compier

:: DOWNLOAD

ROADTRIPS

:: MORE INFORMATION

Citation

Thornton T., McPeek M. S.
“ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure” (2010)
American Journal of Human Genetics, vol 86, pp. 172-184.

Pedcheck 1.00 – Detecting Marker Typing Incompatibilities in Pedigree Data

Pedcheck 1.00

:: DESCRIPTION

PedCheck is a program for identification of genotype incompatibilities in linkage analysis.It will assist researchers in identifying all Mendelian inconsistencies in pedigree data and will provide them with useful and detailed diagnostic information to help resolve the errors.

::DEVELOPER

Division of Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

SunOS / WIndows/MacPPC
C++ Compiler

:: DOWNLOAD

Pedcheck

:: MORE INFORMATION

Citation:

O’Connell JR, Weeks DE,
“PedCheck: A program for identifying genotype incompatibilities in linkage analysis,”
Am J Hum Genet 63:259-266

HaploPainter 1.043 – Pedigree and Haploytype Drawing Tool

HaploPainter 1.043

:: DESCRIPTION

HaploPainter is a user-friendly pedigree-drawing application with special features for easy visualization of complex haplotype information. It has been developed to facilitate gene mapping in Mendelian diseases in terms of fast and reliable definition of the smallest critical interval harbouring the underlying gene defect.

::DEVELOPER

The Gene Mapping Center (GMC)

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Perl

:: DOWNLOAD

HaploPainter

:: MORE INFORMATION

Citation:

Holger Thiele and Peter Nürnberg (2004)
HaploPainter: a tool for drawing pedigrees with complex haplotypes Bioinformatics.
2005 Apr 15;21(8):1730-2. Epub 2004 Sep 17.