GVCHAP 2.1 – Genomic Prediction and Variance Component Estimation Using Haplotypes and SNP Markers

GVCHAP 2.1

:: DESCRIPTION

GVCHAP is a computing pipeline for genomic prediction and variance component estimation using haplotypes and SNP markers.

::DEVELOPER

JOHN GARBE AND YANG DA , Department of Animal Science, University of Minnesota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

GVCHAP

:: MORE INFORMATION

Citation

Prakapenka D, Wang C, Liang Z, Bian C, Tan C, Da Y.
GVCHAP: A Computing Pipeline for Genomic Prediction and Variance Component Estimation Using Haplotypes and SNP Markers.
Front Genet. 2020 Apr 7;11:282. doi: 10.3389/fgene.2020.00282. PMID: 32318093; PMCID: PMC7154123.

HapReads – Infering Haplotypes with Shot Reads

HapReads

:: DESCRIPTION

HapReads is a ILP program for infering haplotypes with shot reads, which finds the most likely haplotypes by approximating local genealogical history as a perfect phylogeny.

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HapReads

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2011:288-99.
Haplotype inference from short sequence reads using a population genealogical history model.
Zhang J1, Wu Y.

DoRIS 0.1 – Demographic Inference based on shared IBD Haplotypes

DoRIS 0.1

:: DESCRIPTION

DoRIS is a Java software tool for demographic inference based on shared IBD haplotypes

::DEVELOPER

Palamara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Java

:: DOWNLOAD

 DoRIS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i180-8. doi: 10.1093/bioinformatics/btt239.
Inference of historical migration rates via haplotype sharing.
Palamara PF1, Pe’er I.

HapFlow 1.1.2 – Visualising Haplotypes in Sequencing Data

HapFlow 1.1.2

:: DESCRIPTION

HapFlow is a python application for visualising haplotypes present in sequencing data. It identifies variant profiles present and reads and creates an abstract visual representation of these profiles to make haplotypes easier to identify.

::DEVELOPER

Mitchell J Sullivan

:: SCREENSHOTS

HapFlow

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 HapFlow

:: MORE INFORMATION

Citation:

HapFlow: Visualising haplotypes in sequencing data.
Sullivan MJ, Bachmann NL, Timms P, Polkinghorne A.
Bioinformatics. 2015 Oct 7. pii: btv551.

Sampling 0.5 – Simulate Haplotypes in Non-Equilibrium Subdivided Populations

Sampling 0.5

:: DESCRIPTION

Sampling is a software for simulating haplotypes in non-equilibrium subdivided populations.

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C Compiler

:: DOWNLOAD

 Sampling

:: MORE INFORMATION

Citation

Thomas Städler, Bernhard Haubold, Carlos Merino, Wolfgang Stephan, and Peter Pfaffelhuber
The impact of sampling schemes on the site-frequency spectrum in non-equilibrium subdivided populations
Genetics May 2009 vol. 182 no. 1 205-216

CHROMIBD 1.1 – Estimation of Identity-by-Descent Probabilities between Haplotypes and Genotyped Ancestors

CHROMIBD 1.1

:: DESCRIPTION

CHROMIBD computes IBD probabilities between a “target chromosome” and a set of “parental chromosomes” (the method works best without “phantom parental chromosomes”). These chromosomes need to be phased and the program relies only on phased (non-missing) markers in target and parental chromosomes. The program works only with bi-allelic markers such as SNPs.

::DEVELOPER

Unit of Animal Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CHROMIBD

:: MORE INFORMATION

Citation

T. Druet and F. Farnir (2011)
Modeling of identity-bydescent processes along a chromosome between haplotypes and their genotyped ancestors.
Genetics. 2011 June; 188(2): 409–419.