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.

hapassoc 1.2-8 – Inference of Trait Associations with SNP Haplotypes and other attributes using the EM Algorithm

hapassoc 1.2-8

:: DESCRIPTION

The hapassoc R package implementing methods described in Burkett et al. (2004) for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm.

::DEVELOPER

SFU Statistical Genetics working group

:: REQUIREMENTS

:: DOWNLOAD

 hapassoc

:: MORE INFORMATION

Citation

Burkett et al. (2004)
A note on inference of trait associations with SNP haplotypes and other attributes in generalized linear models.
Hum Hered. 2004;57(4):200-6.

MOCSphaser – Infer Haplotypes composed of Copy Numbers Alleles and SNP Alleles

MOCSphaser

:: DESCRIPTION

MOCSphaser is a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 MOCSphaser

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1645-6. doi: 10.1093/bioinformatics/btn242. Epub 2008 May 20.
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
Kato M1, Nakamura Y, Tsunoda T.

HaploShare 1.02 – Find Shared Haplotypes among Patients from a common recent Ancestor

HaploShare 1.02

:: DESCRIPTION

HaploShare was designed to find shared haplotypes among patients from a common recent ancestor.

::DEVELOPER

Paed Lab @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HaploShare

:: MORE INFORMATION

Rehh 1.13 – Search for Footprints of Selection using Haplotype Homozygosity based tests

Rehh 1.13

:: DESCRIPTION

Rehh is an R package to search for footprints of selection using Haplotype Homozygosity based tests

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • R

:: DOWNLOAD

 Rehh

:: MORE INFORMATION

Citation

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.
Gautier M, Vitalis R.
Bioinformatics. 2012 Apr 15;28(8):1176-7. doi: 10.1093/bioinformatics/bts115.

PiCNV 0.1 – Phasing normal and CNV-carrying Haplotypes of CNV Regions in Families

PiCNV 0.1

:: DESCRIPTION

PiCNV (Phasing and inheritance of Copy Number Variants) enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data.

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PiCNV

:: MORE INFORMATION

Citation:

PLoS One. 2015 Apr 8;10(4):e0122713. doi: 10.1371/journal.pone.0122713. eCollection 2015.
Haplotype phasing and inheritance of copy number variants in nuclear families.
Palta P, Kaplinski L, Nagirnaja L, Veidenberg A, Möls M, Nelis M, Esko T, Metspalu A, Laan M, Remm M

ParaHaplo 4.0 beta – Tools for Haplotype-based Whole-genome Association Study using Parallel Computing

ParaHaplo 4.0 beta

:: DESCRIPTION

ParaHaplo is developing parallel computing tools for genome-wide association studies.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • OpenMPI version 1.2.5, or MPICH version 1.2.7p1

:: DOWNLOAD

 ParaHaplo

:: MORE INFORMATION

Citation

ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing.
Misawa K, Kamatani N.
Source Code Biol Med. 2011 May 24;6(1):10. doi: 10.1186/1751-0473-6-10.

CNVphaser / CNVphaserPro 1.1 – Infer CNV Haplotypes with Variations

CNVphaser / CNVphaserPro 1.1

:: DESCRIPTION

CNVphaser infers haplotypes with variations in both copy numbers and nucleotide sequences within a CNV region

CNVphaserPro, a successor of CNVphaser and MOCSphaser to handle noisy CNV data such as microarray data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 CNVphaser / CNVphaserPro

:: MORE INFORMATION

Citation

Am J Hum Genet. 2008 Aug;83(2):157-69. doi: 10.1016/j.ajhg.2008.06.021. Epub 2008 Jul 17.
An algorithm for inferring complex haplotypes in a region of copy-number variation.
Kato M1, Nakamura Y, Tsunoda T.

WinHAP 2.0 – Fast Haplotype Phasing program for long Genotype Sequences

WinHAP 2.0

:: DESCRIPTION

WinHAP is a fast haplotype phasing program for phasing large-scale population genotypes data. WinHAP2.0 is a significantly improved version of the WinHAP program that both process longer sequences with less computer memory usage and increases computing speed.

::DEVELOPER

Weihua Pan, Yun Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 WinHAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 30;15(1):164. [Epub ahead of print]
WinHAP2: an extremely fast haplotype phasing program for long genotype sequences.
Pan W, Zhao Y, Xu Y, Zhou F.

PLoS One. 2012;7(8):e43163. doi: 10.1371/journal.pone.0043163. Epub 2012 Aug 14.
WinHAP: an efficient haplotype phasing algorithm based on scalable sliding windows.
Xu Y1, Cheng W, Nie P, Zhou F.