Tag: Haplotype

inPHAP 1.1 – Interactive Phased Haplotype Visualization

inPHAP  1.1

:: DESCRIPTION

inPHAP is an interactive phased haplotype visualization tool, featuring a variety of interaction possibilities such as zooming, sorting, filtering and aggregation of rows in order to explore patterns hidden in large genetic datasets.

::DEVELOPER

Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen

:: SCREENSHOTS

iPHAP

:: REQUIREMENTS

  • Linux/MacOS / Windows
  • Java

:: DOWNLOAD

 inPHAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jul 10;15:200. doi: 10.1186/1471-2105-15-200.
inPHAP: interactive visualization of genotype and phased haplotype data.
Jäger G1, Peltzer A, Nieselt K.

GPMAP – Global Haplotype Partitioning for Maximal Associated SNP Pairs

GPMAP

:: DESCRIPTION

GPMAP has been developed based on the open source code of Haploview (ver. 4.1). Therefore GPMAP basically inherits all Haploview functions plus the global partitioning method

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

GPMAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Aug 27;10:269. doi: 10.1186/1471-2105-10-269.
Global haplotype partitioning for maximal associated SNP pairs.
Katanforoush A1, Sadeghi M, Pezeshk H, Elahi E.

iXora – Exact Haplotype Inferencing and Trait Association

iXora

:: DESCRIPTION

iXora  (Identifying crossovers and recombining alleles) is a framework for inferring haplotypes from genotyped population data, and for associating observed phenotypes with the inferred haplotypes

::DEVELOPER

iXora Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 iXora 

:: MORE INFORMATION

Citation

iXora: exact haplotype inferencing and trait association.
Utro F, Haiminen N, Livingstone D 3rd, Cornejo OE, Royaert S, Schnell RJ, Motamayor JC, Kuhn DN, Parida L.
BMC Genet. 2013 Jun 6;14:48. doi: 10.1186/1471-2156-14-48.

GSA-SNP 20130719 – Process SNP data as well as Gene and Haplotype data

GSA-SNP 20130719

:: DESCRIPTION

GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.

::DEVELOPER

Dr. Dougu Nam , Dr. Sangsoo Kim

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 GSA-SNP

:: MORE INFORMATION

Citation

GSA-SNP: a general approach for gene set analysis of polymorphisms.
Nam D, Kim J, Kim SY, Kim S.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W749-54. doi: 10.1093/nar/gkq428. Epub 2010 May 25.

HapEvolution – Detect Gene-gene Interactions from Case-control Haplotype data

HapEvolution

:: DESCRIPTION

HapEvolution is a cooperative coevolutionary algorithm (CCA) to detect gene-gene interactions from case-control haplotype data; moreover, this algorithm can tolerate up to 15% missing/ambiguous positions in haplotype data arising during haplotype phasing from genotypes. Further, the algorithm can compute epistatic associations from genes spanning multiple chromosomes.

::DEVELOPER

Population Therapeutics Research Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

  HapEvolution

:: MORE INFORMATION

SNaP – Simulation of sNp haplotype data And Phenotypic traits

SNaP

:: DESCRIPTION

The SNaP program can be used to generate SNP haplotype sequence data of unrelated individuals and nuclear families with a fixed or random number of children.

::DEVELOPER

Statistical Genetics and Bioinformatics Group, Cologne Center for Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows
:: DOWNLOAD

  SNaP

:: MORE INFORMATION

Citation

Nothnagel M (2002).
Simulation of LD block-structured SNP haplotype data and its use for the analysis of case-control data by supervised learning methods.
Am J Hum Genet 71 (Suppl.)(4): A2363.

Haploscribe 0.1.0 – Chromosomal Haplotypes by Genetic Phasing of Human Families

Haploscribe 0.1.0

:: DESCRIPTION

Haploscribe is a software package that uses Whole Genome Next Generation Sequencing data from a nuclear family to phase the genomic data into haplotypes spanning entire chromosomes.

::DEVELOPER

Family Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  Haploscribe

:: MORE INFORMATION

Citation

Am J Hum Genet. 2011 Sep 9;89(3):382-97. doi: 10.1016/j.ajhg.2011.07.023.
Chromosomal haplotypes by genetic phasing of human families.
Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF.

HAPI-UR 1.01 – HAPlotype Inference for UnRelated samples

HAPI-UR 1.01

:: DESCRIPTION

HAPI-UR is a program for inferring phased haplotypes from unphased genotypes

::DEVELOPER

Reich laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HAPI-UR

:: MORE INFORMATION

Citation

Am J Hum Genet. 2012 Aug 10;91(2):238-51. doi: 10.1016/j.ajhg.2012.06.013.
Phasing of many thousands of genotyped samples.
Williams AL, Patterson N, Glessner J, Hakonarson H, Reich D.

GLASCOW – Haplotype-based Association Mapping for Binary Traits in Structured Populations

GLASCOW

:: DESCRIPTION

GLASCOW performs genome-wide association studies using Generalized Linear Mixed Models (GLMM) and a score test as described in Zhang et al. Association is performed between factors (SNPs or haplotypes) and a phenotype (with different type of distributions:normal, binomial, counts). The method relies on two steps. In the first one, a GLMM without the factor of interest is solved (including estimation of variance components and of fixed and random effects solutions) and residuals are computed. In the second step, the residuals are used to test significance of association between the factor and the phenotype at each position along the genome (or the selected data).

::DEVELOPER

Unit of Animal Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GLASCOW

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 1;28(19):2467-73. Epub 2012 Jun 17.
Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification.
Zhang Z, Guillaume F, Sartelet A, Charlier C, Georges M, Farnir F, Druet T.

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