MIXMUL – Estimating Haplotype Frequencies and Reconstructing Haplotypes from Mixed Genotype Data

MIXMUL

:: DESCRIPTION

MIXMUL (Mixture of Weighted Multinomial) procedure is a convenient haplotype inference tool for mixed data to estimate haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

 MIXMUL

:: MORE INFORMATION

Citation

J Biomed Sci. 2009 Jun 2;16:52. doi: 10.1186/1423-0127-16-52.
A novel tool for individual haplotype inference using mixed data.
Lin CP, Fann CS.

MutaGeneSys 20071020 – Use Genome-wide Genotype Data to Estimate Individual Disease

MutaGeneSys 20071020

:: DESCRIPTION

MutaGeneSys  (Mutation Genome System) uses genome-wide genotype data to estimate individual disease susceptibility. Our system integrates three data sources: the International HapMap project(hapmap.org), whole-genome marker correlation data (description) and the Online Mendelian Inheritance in Man database (OMIM). MutaGeneSys accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. Our system produces population, genotyping technology, and confidence-specific predictions in interactive time.

::DEVELOPER

Julia Stoyanovich 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MutaGeneSys

:: MORE INFORMATION

Citation:

Julia Stoyanovich and Itsik Pe’er 2008.
MutaGeneSys: Making Diagnostic Predictions Based on Genome-Wide Genotype Data in Association Studies
Bioinformatics (2008) 24 (3): 440-442

SEQERR – Estimates Genotype Error Rates for Whole-genome Sequence data

SEQERR

:: DESCRIPTION

The SEQERR program estimates the rate at which homozygous major allele genotypes are mis-called as heterozygote genotypes at low frequency markers. This error rate is estimated using observed allele and genotype frequencies at low frequency variants in identity by descent segments.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

SEQERR

:: MORE INFORMATION

Citation:

Browning SR, Browning BL.
Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent.
Am J Hum Genet. 2015 Sep 3;97(3):404-18. doi: 10.1016/j.ajhg.2015.07.012. Epub 2015 Aug 20. PMID: 26299365; PMCID: PMC4564943.

ADMIXMAP 3.8.3103 – Model Admixture using Marker Genotype data

ADMIXMAP 3.8.3103

:: DESCRIPTION

ADMIXMAP (Admixture mapping)is a general-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus.

::DEVELOPER

Paul McKeigue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

  ADMIXMAP

:: MORE INFORMATION

Citation:

Carcinogenesis. 2011 Mar;32(3):312-7. Epub 2010 Nov 29.
Admixture mapping of lung cancer in 1812 African-Americans.
Schwartz AG et al.

Gigwa 2.4.1 – Genotype Investigator for Genome Wide Analyse

Gigwa 2.4.1

:: DESCRIPTION

The Gigwa application provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time.

:: DEVELOPER

South Green bioinformatics platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

Gigwa

:: MORE INFORMATION

Citation

Gigwa v2-Extended and improved genotype investigator.
Sempéré G, Pétel A, Rouard M, Frouin J, Hueber Y, De Bellis F, Larmande P.
Gigascience. 2019 May 1;8(5). pii: giz051. doi: 10.1093/gigascience/giz051.

Gigwa-Genotype investigator for genome-wide analyses.
Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P.
Gigascience. 2016 Jun 6;5:25. doi: 10.1186/s13742-016-0131-8.

DRBTool – Determine HLA Genotypes at the DRB1 locus

DRBTool

:: DESCRIPTION

DRBTool supports a new technique for determining HLA genotypes at the DRB1 locus through non-electrophoretic scoring of group-specific PCR.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows
  • MS SQL

:: DOWNLOAD

 DRBTool

:: MORE INFORMATION

Citation

Hampe J, Valentonyte R, Manaster C, Teuber M, Jenisch S, Entz P, Nagy M, Schreiber S (2004).
Nonelectrophoretic method for high-throughput HLA-DRB1 group genotyping.
BioTechniques 36: 148-151

CNGen 1.0.1 – Convert Integrated SNP and CNV Calls into Phased Copy Number Genotypes

CNGen 1.0.1

:: DESCRIPTION

CNGen is a scritp that converts integrated SNP and CNV calls generated from Birdsuite ‘s Fawkes procedure into phased copy number genotypes (CN genotypes) using familial pedigree data. This software makes possible the use of CNPs and CNVs for genetic linkage with family data.

::DEVELOPER

Marie-Pierre Dubé’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Python

:: DOWNLOAD
 CNGen

:: MORE INFORMATION

MULTIPRED2 – large-scale Screening of allele-, genotype-, and supertype-specific HLA Associated Peptides

MULTIPRED2

:: DESCRIPTION

MULTIPRED2 is a computational system for large-scale screening of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR supertypes as well as to alleles belonging to an individual’s genotype.

::DEVELOPER

MULTIPRED2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Immunol Methods. 2011 Nov 30;374(1-2):53-61. doi: 10.1016/j.jim.2010.11.009. Epub 2010 Dec 2.
MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles.
Zhang GL1, DeLuca DS, Keskin DB, Chitkushev L, Zlateva T, Lund O, Reinherz EL, Brusic V.

Admixture 1.3.0 – Fast Ancestry Estimation

Admixture 1.3.0

:: DESCRIPTION

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.

::DEVELOPER

David Alexander

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

Admixture

:: MORE INFORMATION

Citation

Fast model-based estimation of ancestry in unrelated individuals.
Alexander DH, Novembre J, Lange K.
Genome Res. 2009 Sep;19(9):1655-64. doi: 10.1101/gr.094052.109.

BMC Bioinformatics. 2011 Jun 18;12:246. doi: 10.1186/1471-2105-12-246.
Enhancements to the ADMIXTURE algorithm for individual ancestry estimation.
Alexander DH, Lange K.

DeepGS 1.2 – Predicting Phenotypes from Genotypes using Deep Learning

DeepGS 1.2

:: DESCRIPTION

DeepGS is a R package for predicting phenotypes from genotypes using deep learning techniques.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

DeepGS

:: MORE INFORMATION

Citation

Ma W, Qiu Z, Song J, Li J, Cheng Q, Zhai J, Ma C.
A deep convolutional neural network approach for predicting phenotypes from genotypes.
Planta. 2018 Nov;248(5):1307-1318. doi: 10.1007/s00425-018-2976-9. Epub 2018 Aug 12. PMID: 30101399.

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