:: DESCRIPTION
VASP is a standalone perl software package designed to analyse sequenced pedigrees.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Reducing the search space for causal genetic variants with VASP: Variant Analysis of Sequenced Pedigrees.
Field MA, Cho V, Cook MC, Enders A, Vinuesa C, Whittle B, Andrews TD, Goodnow CC.
Bioinformatics. 2015 Mar 8. pii: btv135.
:: DESCRIPTION
PBAP is a pipeline for file processing and quality control of pedigree data with dense genetic markers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PBAP: A pipeline for file processing and quality control of pedigree data with dense genetic markers.
Nato AQ Jr, Chapman NH, Sohi HK, Nguyen HD, Brkanac Z, Wijsman EM.
Bioinformatics. 2015 Jul 30. pii: btv444.
:: DESCRIPTION
famSKAT-RC is an R scripts to carry out a combined rare- and common-variant gene-based test of association in the presence of related individuals.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genet Epidemiol. 2014 Nov;38(7):579-90. doi: 10.1002/gepi.21844. Epub 2014 Aug 1.
Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees.
Saad M1, Wijsman EM.
:: DESCRIPTION
plotIBD is a perl script to assist with plotting sampled inheritance vectors in pedigrees
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hum Hered. 2011;72(4):289-97. doi: 10.1159/000334083. Epub 2011 Dec 23.
Estimation and visualization of identity-by-descent within pedigrees simplifies interpretation of complex trait analysis.
Marchani EE1, Wijsman EM.
:: DESCRIPTION
PRIMUS is a pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PRIMUS: Improving Pedigree Reconstruction using Mitochondrial and Y Haplotypes.
Staples J, Ekunwe L, Lange E, Wilson JG, Nickerson DA, Below JE.
Bioinformatics. 2015 Oct 29. pii: btv618
:: DESCRIPTION
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.
::DEVELOPER
the Center of Biomedicine (CBM) at EURAC research.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fuchsberger, Falchi, Forer, Pramstaller (2007),
“PedVizApi: A Java API for the interactive, visual analysis of extended pedigrees“,
Bioinformatics, 24(2):279-281
:: DESCRIPTION
reHCstar is a SAT-based program to compute a haplotype configuration on pedigrees with recombinations, genotyping errors, and missing genotypes.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, and Paola Bonizzoni.
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2012).
:: DESCRIPTION
Heu-MCHC is a fast and accurate heuristic for the Minimum-Change Haplotype Configuration (MCHC) problem, i.e. a combinatorial formulation of the haplotype inference problem on pedigree data where the total number of recombinations and point mutations has to be minimized.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yuri Pirola, Paola Bonizzoni, and Tao Jiang.
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume: 9 , Issue: 1 Page(s): 12 – 25 (2011).
:: DESCRIPTION
PedCut is a program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size
::DEVELOPER
Group of the Methods of Genetic Analysis
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Eur J Hum Genet. 2008 Jul;16(7):854-60. doi: 10.1038/ejhg.2008.24. Epub 2008 Feb 27.
An approach for cutting large and complex pedigrees for linkage analysis.
Liu F, Kirichenko A, Axenovich TI, van Duijn CM, Aulchenko YS.
:: DESCRIPTION
VIPER (Visual Pedigree Explorer) combines an improved ResSpecies algorithm for genotype inheritance checking and inference with a novel space-efficient visualisation of pedigree structure in a desktop tool for exploring then cleaning data errors in pedigree/genotype datasets.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012;13 Suppl 8:S5. doi: 10.1186/1471-2105-13-S8-S5. Epub 2012 May 18.
VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.
Paterson T, Graham M, Kennedy J, Law A.
