Hapi 1.03 – Rapid Haplotype Inference for Nuclear Families

Hapi 1.03

:: DESCRIPTION

Hapi is a program that efficiently infers minimum recombinant and maximum likelihood haplotypes for nuclear families.

::DEVELOPER

Williams lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Hapi

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(10):R108. doi: 10.1186/gb-2010-11-10-r108. Epub 2010 Oct 29.
Rapid haplotype inference for nuclear families.
Williams AL, Housman DE, Rinard MC, Gifford DK.

HAPAR – Haplotype Inference by Parsimony

HAPAR

:: DESCRIPTION

HAPAR (Haplotype Inference by Parsimony) is a program to infer haplotype from genotype data. It uses the parsimony principle, i.e. try to find the minimum number of haplotypes that can reconstruct the input genotypes.

::DEVELOPER

Lusheng Wang ,  Ying Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /UNIX

:: DOWNLOAD

 HAPAR

:: MORE INFORMATION

Citation

Lusheng Wang, Ying Xu,
Haplotype Inference by Parsimony,
Bioinformatics, 19(14), 2003.

DSS – Haplotype Inference for Large Families

DSS

:: DESCRIPTION

DSS is a software for haplotype inference for large families

::DEVELOPER

Xin Li 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 DSS

:: MORE INFORMATION

Citation

Xin Li and Jing Li.
An Almost Linear Time Algorithm for a General Haplotype Solution on Tree Pedigrees with no Recombination and its Extensions.
Journal of Bioinformatics and Computational Biology 7(3):521-545, 2009.

PedPhase 3.0 – Haplotype Inference from Genotypes on Pedigree data

PedPhase 3.0

:: DESCRIPTION

PedPhase is a suite of computer programs for haplotype inference from genotypes on pedigree data. It consists of several different algorithms that are designed based on a combinatorial formulation of haplotype inference, namely the minimum-recombinant haplotype configuration (MRHC) problem, and are effective for different types of data.

::DEVELOPER

Computational Biology lab @ Case (CBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PedPhase

:: MORE INFORMATION

Citation

Li X, Li J.
An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions.
J Bioinform Comput Biol. 2009 Jun;7(3):521-45.

HaploHMM 20140622 – Hidden Markov Model (HMM) Based Program for Haplotype Inference

HaploHMM 20140622

:: DESCRIPTION

HaploHMM is a Hidden Markov Model (HMM) based program for haplotype inference using identified haplotypes and haplotype patterns

::DEVELOPER

Kui Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HaploHMM

:: MORE INFORMATION

Citation

Front Genet. 2014 Aug 12;5:267. doi: 10.3389/fgene.2014.00267. eCollection 2014.
A hidden Markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns.
Wu J, Chen GB, Zhi D, Liu N, Zhang K.

reHCstar 2.1.5 – Algorithm for Haplotype Inference problem on Pedigree data with Recombinations, Errors and Mutations

reHCstar 2.1.5

:: DESCRIPTION

reHCstar is a SAT-based program to compute a haplotype configuration on pedigrees with recombinations, genotyping errors, and missing genotypes.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • CMake
  • GNU make
  • Boost FileSystem, System, DateTime, ProgramOptions, IOStreams, and other include-only libraries
  • Apache Log4cxx

:: DOWNLOAD

 reHCstar

:: 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).

Heu-MCHC 1.0.2 – Heuristic Algorithm for the Haplotype Inference problem on Pedigree data with recombinations and mutations

Heu-MCHC 1.0.2

:: 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

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 Heu-MCHC 

:: 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).

RPOLY 1.2.1 – Inference of Haplotypes by Pure Parsimony

RPOLY 1.2.1

:: DESCRIPTION

RPoly is a software to infer haplotypes from genotype data using the pure parsimony criterion, i.e., find the minimum number of haplotypes which explain a given set of genotypes. Rpoly is an efficient tool which uses pseudo-Boolean optimization to solve haplotype inference by pure parsimony.

::DEVELOPER

Ana Sofia Graça

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 RPoly

:: MORE INFORMATION

Citation

A. Graça, J. P. Marques-Silva, I. Lynce and A. Oliveira,
Efficient Haplotype Inference with Pseudo-Boolean Optimization,
Algebraic Biology 2007, July 2007.

A. Graça, J. P. Marques-Silva, I. Lynce and A. Oliveira,
Efficient Haplotype Inference with Combined CP and OR Techniques (Short Paper),
CPAIOR 2008, May 2008.

SATlotyper 0.1.5 – Haplotype Inference from unphased SNP data in Heterozygous Polyploids based on SAT

SATlotyper 0.1.5

:: DESCRIPTION

 SATlotyper is a software tool designed for inferring haplotypes from polyploid and polyallelic unphased SNP data.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

  SATlotyper

:: MORE INFORMATION

Citation

Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT.
Neigenfind J, Gyetvai G, Basekow R, Diehl S, Achenbach U, Gebhardt C, Selbig J, Kersten B.
BMC Genomics. 2008 Jul 30;9:356.

SDPHapInfer / LongHapInfer – Software for Haplotype Inference

SDPHapInfer / LongHapInfer

:: DESCRIPTION

The SDPHapInfer formulates the haplotype inference problem as the following integer quadratic programming (IQP) problem. The objective function is to minimize the number of haplotypes, and the constraint functions are to resolve each genotype.

LongHapInfer partitions the genotypes into segments, infers subhaplotypes for each segment, and concatenates subhaplotypes in different segments for the final solution.

::DEVELOPER

Kun-Mao Chao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SDPHapInfer / LongHapInfer

:: MORE INFORMATION

Citation

Huang, Y.-T., Chao, K.-M., and Chen, T., 2005,
An Approximation Algorithm for Haplotype Inference by Maximum Parsimony,”
Journal of Computational Biology, 12: 1261-1274.