HIERFSTAT 0.5-10 – Package for R to Compute & Test Hierarchical F-statistics

HIERFSTAT 0.5-10

:: DESCRIPTION

HIERFSTAT is a package for R allowing to estimate F-statistics and variance components with the methods of moments for any number of levels in a hierarchy. The package also allows to test the significance of population differentiation using the likelihood ratio G-statistic or the variance components.

::DEVELOPER

Jérôme Goudet.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS
R package

:: DOWNLOAD

HIERFSTAT

:: MORE INFORMATION

Citation

Goudet, J. (2005)
Hierfstat, a package for R to compute and test hierarchical F-statistics.
Molecular Ecology Notes. 5: 184-186

Xmipp 3.1 – X-Windows-based Microscopy Image Processing Package

Xmipp 3.1

:: DESCRIPTION

Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.

::DEVELOPER

Biocomputing Unit

:: SCREENSHOTS

:: REQUIREMENTS

Windows with Cygwin /Linux/MacOsX
Python

:: DOWNLOAD

Xmipp

:: MORE INFORMATION

Citation

de la Rosa-Trevín JM, Otón J, Marabini R, Zaldívar A, Vargas J, Carazo JM, Sorzano CO.
Xmipp 3.0: an improved software suite for image processing in electron microscopy.
J Struct Biol. 2013 Nov;184(2):321-8. doi: 10.1016/j.jsb.2013.09.015. Epub 2013 Sep 26. PMID: 24075951.

C.O.S. Sorzano, R. Marabini, J.M. Carazo, J. Velazquez-Muriel, J.R. Bilbao-Castro, S.H.W. Scheres, J.M. Carazo and A. Pascual-Montano.
XMIPP: A new generation of an open-source image processing package for Electron Microscopy.
J Struct Biol. 2004 Nov;148(2):194-204.

Chaplin 1.2.3 – Case-control Haplotype Inference package

Chaplin 1.2.3

:: DESCRIPTION

Chaplin (Case-control haplotype inference package.) is a software program for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study.

::DEVELOPER

Epstein software

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Chaplin

:: MORE INFORMATION

Citation

Epstein MP and Satten GA (2003).
Inference on haplotype effects in case-control studies using unphased genotype data.
Am. J. Hum. Genet. 73:1316-1329

Satten GA and Epstein MP (2004).
Comparison of prospective and retrospective methods for haplotype inference in case-control studies.
Genet Epidemiol. 2004 Nov; 27(3):192-201

RSeQC v3.0.1 – RNA-seq Quality Control package

RSeQC v3.0.1

:: DESCRIPTION

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
Python

:: DOWNLOAD

RSeQC

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27.
RSeQC: quality control of RNA-seq experiments.
Wang L, Wang S, Li W.

Fiji 20141125 – Image Processing Package based on ImageJ

Fiji 20141125

:: DESCRIPTION

Fiji (Fiji is Just ImageJ) is an image processing package. It can be described as a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure.

::DEVELOPER

Fiji Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

Fiji

:: MORE INFORMATION

Publications introducing Fiji

R/gap 1.1-3 – R/Genetic Analysis Package

R/gap 1.1-3

:: DESCRIPTION

R/gap (R/Genetic Analysis Package) is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

::DEVELOPER

Jing Hua Zhao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOSX
R Package

:: DOWNLOAD

R/gap

:: MORE INFORMATION

Eip 1.0 – Epistatic Interaction Package

Eip 1.0

:: DESCRIPTION

The Eip( Epistatic Interaction Package) is developed to estimate the epistatic effector in a candidate-gene case-control data set based on the Tian’s model

::DEVELOPER

Center for Statistical Genetics, Penn State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows /Linux/ MacOsX
R package

:: DOWNLOAD

Eip

:: MORE INFORMATION

Citation

Zhong Wang, Zhenwu Lin, Arthur Berg, John Hegarty, Walter A. Koltun and Rongling Wu.
A general model for multilocus epistatic interactions in Case-Control studies.
PLoS ONE 5(8): e11384. doi:10.1371/journal.pone.0011384

Ghemical 3.0.0 – Molecular Modeling and Editing Package for GNOME

Ghemical 3.0.0

:: DESCRIPTION

Ghemical is a molecular modeling and editing package for GNOME. It integrates a molecular mechanics force field as well as integration with MOPAC and optionally the MPQC package for quantum mechanical calculations. It integrates Open Babel to import/export to a variety of external programs.

::DEVELOPER

Ghemical Team

:: SCREENSHOTS

:: REQUIREMENTS

Linux
GNOME

:: DOWNLOAD

Ghemical

:: MORE INFORMATION

Citation

Tommi Hassinen, Mikael Peräkylä:
New energy terms for reduced protein models implemented in an off-lattice force field.
J Comput Chem 2001 , 22, 1229-1242

PHASE 2.0 – Bayesian & Maximum Likelihood Phylogenetic Inference Package

PHASE 2.0

:: DESCRIPTION

PHASE (PHylogenetics And Sequence Evolution) is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.This package is designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. It is well known that compensatory substitutions occur in the paired regions of RNA secondary structures; this means that substitutions occurring on one side of a pair are correlated with substitutions on the other side. Most phylogenetic programs assume that each site in a molecule evolves independently of the others but this assumption is not valid for RNA genes.

::DEVELOPER

Rattray Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS

:: DOWNLOAD

PHASE

:: MORE INFORMATION

Citation

V. Gowri-Shankar and M. Rattray.
A reversible jump method for Bayesian phylogenetic inference with a non-homogeneous substitution model” Molecular Biology and Evolution
Molecular Biology and Evolution 24(6):1286-1299 (2007).

PAP 7.1 /jPAP 1.7.1 – Pedigree Analysis Package

PAP 7.1 /jPAP 1.7.1

:: DESCRIPTION

PAP (Pedigree Analysis Package) is a package of programs for computing likelihoods or simulating phenotypes on pedigree members using genetic models. Version 7.1(1) is the latest release in a long line of console-driven implementations. The package may be used for segregation analysis, variance components analysis, linkage analysis, measured genotype analysis, transmission disequilibrium testing, or genetic model fitting. It is distributed as the FORTRAN source. A large suite of examples, keyed to the manual, is included.

jPAP (Java Pedigree Analysis Package) is a document-driven GUI edition of PAP, intended to replace and extend the older console programs.

::DEVELOPER

Sandra J. Hasstedt

:: SCREENSHOTS

:: REQUIREMENTS

Linux/windows/MacOsX
Java

:: DOWNLOAD

PAP /jPAP

:: MORE INFORMATION

Citation

Hum Hered. 2011;72(4):258-63. Epub 2011 Dec 23.
Detecting pleiotropy and epistasis using variance components linkage analysis in jPAP.
Hasstedt SJ, Thomas A.