Cri-Map 2.4 – Construct Multilocus Linkage Map

Cri-Map 2.4

:: DESCRIPTION

CRI-MAP‘s purpose is to allow rapid, largely automated construction of multilocus linkage maps (and facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors). Although originally designed to handle codominant loci (e.g. RFLPs) scored on pedigrees “without missing individuals”, such as CEPH or nuclear families, it can now (with some caveats described below) be used on general pedigrees, and some disease loci.

::DEVELOPER

Matise Laboratory of Computational Genetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows wity Cygwin /MacOsX
  • GCC
:: DOWNLOAD

  CRI-MAP

:: MORE INFORMATION

Citation

Hum Hered. 1995 Mar-Apr;45(2):103-16.
Parallel computation of genetic likelihoods using CRI-MAP, PVM, and a network of distributed workstations.
Matise TC, Schroeder MD, Chiarulli DM, Weeks DE.

HIPPO 1.0/ AEML 1.0 – Estimate Population Haplotype Frequencies from Pooled SNP data

HIPPO 1.0/ AEML 1.0

:: DESCRIPTION

Hippo (Haplotype estimation under incomplete prior information using pooled observations) is a program for estimating haplotype distribution from pooled DNA data and is able to utilize prior information about the haplotypes that are known to be present in the population.

AEML is a program for estimating haplotype distribution from pooled DNA data and is able to utilize prior information about the haplotypes that are known to be present in the population.

::DEVELOPER

Matti Pirinen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

  HIPPO  – AEML Source Code

:: MORE INFORMATION

Citation

Matti Pirinen
Estimating population haplotype frequencies from pooled SNP data using incomplete database information
Bioinformatics (2009) 25 (24): 3296-3302

Matrix eQTL 2.1.0 – Ultra fast eQTL Analysis via Large Matrix Operations

Matrix eQTL  2.1.0

:: DESCRIPTION

Matrix eQTL can model and test for association using both linear regression and ANOVA models. The models can include covariates to account for such factors as population structure, gender, and clinical variables. It also supports testing of heteroscedastic models and models with correlated errors. In our experiment on large datasets Matrix eQTL was thousands of times faster than the existing popular software for QTL/eQTL analysis.

::DEVELOPER

Andrey A. Shabalin,

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 Matrix eQTL

:: MORE INFORMATION

Citation

Matrix eQTL: ultra fast eQTL analysis via large matrix operations.
Shabalin AA.
Bioinformatics. 2012 May 15;28(10):1353-8. doi: 10.1093/bioinformatics/bts163. Epub 2012 Apr 6.

MetaSKAT 0.81 – Meta-analysis for multiple markers

MetaSKAT 0.81

:: DESCRIPTION

MetaSKAT is a R package for multiple marker meta-analysis across studies. It can carry out meta-analysis of SKAT, SKAT-O and burden tests with individual level genotype data or gene level summary statistics.

::DEVELOPER

Xihong Lin’s Group, Harvard School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  MetaSKAT

:: MORE INFORMATION

Citation

Lee, S., Teslovich, T.M., Boehnke, M. and Lin, X. (2013)
General framework for meta-analysis of rare variants in sequencing association studies
Am J Hum Genet. 2013 Jul 11;93(1):42-53. doi: 10.1016/j.ajhg.2013.05.010

Hapsample 0.12 – Association Simulator for Candidate Regions or Genome Scans

Hapsample 0.12

:: DESCRIPTION

HAP-SAMPLE is an application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be “genotyped,” along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans.

::DEVELOPER

Fei Zou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

Hapsample

:: MORE INFORMATION

Citation

Wright, F.A, Huang, H., Guan, X., Gamiel, K, Jeffries, C., Barry, W.T., de Villena, F.P., Sullivan, P.F., Wilhelmsen, K.C., and Zou. F. (2007)
Simulating association studies: a data-based resampling method for candidate regions or whole genome scans,
Bioinformatics 23: 2581-2588.

RVsharing 1.7.0 – Computes Estimates of the Probability of Related Individuals Sharing a Rare Variant

RVsharing 1.7.0

:: DESCRIPTION

RVsharing computes the probability that a rare variant is shared by related subjects, given that the variant was observed in any of them.

::DEVELOPER

Alexandre Bureau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R

:: DOWNLOAD

 RVsharing

:: MORE INFORMATION

Citation

Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.
Bureau A, Younkin SG, Parker MM, Bailey-Wilson JE, Marazita ML, Murray JC, Mangold E, Albacha-Hejazi H, Beaty TH, Ruczinski I.
Bioinformatics. 2014 Apr 16. pii: btu198.

Evian 2.1.0 – Evidential Analysis of Genetic Association Data

Evian 2.1.0

:: DESCRIPTION

Evian employs the Law of Likelihood, and uses the LR (likelihood ratio)rather than p-values to plan/design, analyze, interpret and replicate genetic association studies.

::DEVELOPER

Strug lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 Evian

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2010 Aug;18(8):933-41. doi: 10.1038/ejhg.2010.47. Epub 2010 Apr 28.
A pure likelihood approach to the analysis of genetic association data: an alternative to Bayesian and frequentist analysis.
Strug LJ1, Hodge SE, Chiang T, Pal DK, Corey PN, Rohde C.

RVS 20140305 – Genetic Association with NGS data

RVS 20140305

:: DESCRIPTION

The RVS (robust variance score) is a novel likelihood-based method for genetic association with NGS data from external control groups. RVS substitutes genotype calls by their expected values given observed sequence data and implements a robust variance estimate for the score statistic.

::DEVELOPER

Strug lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 RVS

:: MORE INFORMATION

Citation

Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic.
Derkach A, Chiang T, Gong J, Addis L, Dobbins S, Tomlinson I, Houlston R, Pal DK, Strug LJ.
Bioinformatics. 2014 Apr 14. pii: btu196.

SXTestPlate 1.0.0 – Analyses Genotypes of a SNPlex™ Control Plate

SXTestPlate 1.0.0

:: DESCRIPTION

SXTestPlate is a Windows program for evaluating the performance of a SNPlex™ genotyping platform by analyzing a test plate, which was typed with a control pool.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

::REQUIREMENTS

  • Windows
  • Microsoft SQL Server

:: DOWNLOAD

 SXTestPlate

:: MORE INFORMATION

Citation

Teuber M, Wenz MH, Schreiber S, Franke A (2009).
GMFilter and SXTestPlate: software tools for improving the SNPlex(TM) genotyping system.
BMC Bioinformatics 10(1):81

SNPSplicer 1.0.0 – Analyse SNP-dependent Splicing in Genotyped cDNAs

SNPSplicer 1.0.0

:: DESCRIPTION

SNPSplicer is a Windows program for the systematic analysis of SNP-dependent splicing in genotyped cDNAs.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows

:: DOWNLOAD

 SNPSplicer

:: MORE INFORMATION

Citation

ElSharawy A, Manaster C, Teuber M, Rosenstiel P, Kwiatkowski R, Huse K, Platzer M, Becker A, Nürnberg P, Schreiber S, Hampe J (2006).
SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs.
Human Mutat 27(11):1129-34