gGranger 1.0.0 – Identification of Granger Causality between Gene Sets

LDWP (Linked Region Detection without Pedigree) is a software package for linkage analysis that finds the mutation regions for the case where the input individuals are closely related, but the pedigree is not known. A typical example is that in the pedigree below the individuals in the dotted rectangle are closely related,and the genotype data of them are known, whereas the genotype data of individuals outside the dotted rectangle are not available and even the pedigree may not be clear. LDWP takes the genotype data of the individuals in the dotted rectangle and the diagnoses (diseased or normal) information of each individual in the dotted rectangle as its input, and report the mutation regions.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

LDWP

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Mar-Apr;9(2):499-510. doi: 10.1109/TCBB.2011.134
Mutation Region Detection for Closely Related Individuals without a Known Pedigree Using High-Density Genotype Data.
Ma W, Yang Y, Chen ZZ, Wang L.

LIden – Linkage Analysis Software

LIden

:: DESCRIPTION

LIden determines allele sharing status among family members using high-density SNP data. It takes SNP genotype data, pedigree structure and physical-locus-file as input, and outputs allele sharing graphical display files and linked regions

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
Java

:: DOWNLOAD

LIden

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jul 15;10:216.
Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference.
Wang L, Wang Z, Yang W.

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.

LUCA 1.0-6 – Likelihood Under Covariate Assumptions

LUCA 1.0-6

:: DESCRIPTION

LUCA (Likelihood Under Covariate Assumptions) is an R package implementing the methods for case-control inference of statistical interaction between genetic and nongenetic risk factors under covariate assumptions.

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

Linux / Windows / MacOsX
R Package

:: DOWNLOAD

LUCA

:: MORE INFORMATION

Citation

Shin et al. (2007)
Case-control inference of interaction between genetic and nongenetic risk factors under assumptions on their distribution
Stat Appl Genet Mol Biol. 2007;6:Article13.

PGEToolbox 3.0 – Matlab Toolbox for Population Genetics and Evolution

PGEToolbox 3.0

:: DESCRIPTION

PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima’s D test, Fu & Li’s tests and Fay & Wu’s H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
MATLAB
MBEToolbox

:: DOWNLOAD

PGEToolbox

:: MORE INFORMATION

Citation:

Cai JJ (2008)
PGEToolbox: A Matlab toolbox for population genetics and evolution
Journal of Heredity Jul-Aug;99(4):438-40. doi:10.1093/jhered/esm127

asSeq 0.99.2 – Statistical Framework for eQTL Mapping using RNA-seq Data

asSeq 0.99.2

:: DESCRIPTION

asSeq is a software of allele specific study of next generation sequencing data, with emphasis on RNA-seq and ChIP-seq data.

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux/Windows/MacOsX
R Package
C Compiler

:: DOWNLOAD

asSeq

:: MORE INFORMATION

Citation

Sun W.
A Statistical Framework for eQTL Mapping Using RNA-seq Data.
Biometrics. 2011 Aug 12.

MBEToolbox 3.0 – MATLAB Molecular Biology & Evolution Toolbox

MBEToolbox 3.0

:: DESCRIPTION

MBEToolbox is a tool which aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned Matlab users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
MATLAB

:: DOWNLOAD

MBEToolbox

:: MORE INFORMATION

Citation:

James J Cai, David K Smith, Xuhua Xia, Kwok-yung Yuen.
MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution
Evolutionary Bioinformatics Online 2006, 2 189-192

BPrimm 1.12 – Bayesian and Penalized Regression in Multiple Loci Mapping

BPrimm 1.12

:: DESCRIPTION

BPrimm (Bayesian and Penalized regression in multiple loci mapping) includes a set of tools for simultaneously multiple loci mapping, and two novel methods named the Bayesian adaptive Lasso and the Iterative Adaptive Lasso

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux/Windows/MacOsX
R Package
C Compiler

:: DOWNLOAD

BPrimm

:: MORE INFORMATION

Citation

Wei Sun, Joseph G. Ibrahim and Fei Zou
Genome-wide Multiple Loci Mapping in Experimental Crosses by the Iterative Adaptive Penalized Regression
Genetics May 2010 vol. 185 no. 1 349-359

Pool-hmm 1.4.2 – Estimating Allele Frequencies and Detecting Selective Sweeps

Pool-hmm 1.4.2

:: DESCRIPTION

Pool-hmm aims at estimating allele frequencies and detecting selective sweeps, using NGS data from a sample of pooled individuals from the same population.

::DEVELOPER

Pool-hmm Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Python

:: DOWNLOAD

Pool-hmm

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2013 Mar;13(2):337-40. doi: 10.1111/1755-0998.12063.
Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.
Boitard S, Kofler R, Fran?oise P, Robelin D, Schl?tterer C, Futschik A.