ENT 1.0.2 – Genotype Phasing by Entropy Minimization

ENT 1.0.2

:: DESCRIPTION

ENT is a highly scalable genotype phasing algorithm based on entropy minimization. ENT is capable of phasing both unrelated and related genotypes coming from complex pedigrees.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux

:: DOWNLOAD

ENT

:: MORE INFORMATION

Citation:

A. Gusev and I.I. Mandoiu and B. Pasaniuc,
Highly Scalable Genotype Phasing by Entropy Minimization,
IEEE/ACM Trans. on Computational Biology and Bioinformatics 5, pp. 252-261, 2008

GEVALT 2.0 – Genotype Analysis

GEVALT 2.0

:: DESCRIPTION

GEVALT (GEnotype Visualization and ALgorithmic Tool) is designed to simplify and expedite the process of genotype analysis and disease association tests by providing a common interface to several common tasks relating to such analyses. It is aimed for analysis of unrelated individuals as well as two-generation families.

::DEVELOPER

Prof. Ron Shamir’s Computational Genomics Laboratory at the School of Computer Science, Tel Aviv University, Israel

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

GEVALT

:: MORE INFORMATION

Citation:

Ofir Davidovich, Gad Kimmel and Ron Shamir.
GEVALT: An integrated software tool for genotype analysis.
BMC Bioinformatics 2007, 8:36.

fastPHASE 1.4.0 – Haplotype Reconstruction & Estimating Missing Genotypes

fastPHASE 1.4.0

:: DESCRIPTION

fastPHASE is a software for haplotype reconstruction, and estimating missing genotypes from population data. fastPHASE can handle larger data-sets than PHASE (e.g., hundreds of thousands of markers in thousands of individuals), but does not provide estimates of recombination rates.

::DEVELOPER

Matthew Stephens Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac

:: DOWNLOAD

fastPHASE

:: MORE INFORMATION

The software is free for non-commercial use, and may be licensed for commercial use.

Citation

Scheet, P and Stephens, M (2006) A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase. Am J Hum Genet 78: 629-644

sampletrees 20151127 / Rsampletrees 1.0.3 – Sampling Gene Genealogies Conditional on SNP Genotype data

sampletrees 20151127 / Rsampletrees 1.0.3

:: DESCRIPTION

The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

Linux / Windows / MacOsX
R Package

:: DOWNLOAD

sampletrees / Rsampletrees

:: MORE INFORMATION

Citation

sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data.
Burkett KM, McNeney B, Graham J.
Bioinformatics. 2016 Jan 18. pii: btv763.