Tag: Analysis

GCTA 1.01 – Genome-wide Complex Trait Analysis

GCTA 1.01

:: DESCRIPTION

GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits

::DEVELOPER

Peter Visscher’s lab at the Queensland Institute of Medical Research .

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /MacOsX /  Linux

:: DOWNLOAD

 GCTA

:: MORE INFORMATION

Citation

Yang J, Lee SH, Goddard ME and Visscher PM.
GCTA: a tool for Genome-wide Complex Trait Analysis.
Am J Hum Genet. 2011 Jan 88(1): 76-82

GenAlEx 6.51b2 – Population Genetic Analysis within Microsoft Excel

GenAlEx 6.51b2

:: DESCRIPTION

GenAlEx (Genetic Analysis in Excel) is a user-friendly cross-platform package for population genetic analysis that runs within Microsoft Excel(TM). GenAlEx enables population genetic data analysis of codominant, haploid and binary genetic data providing analysis tools applicable to plants, animals and microorganisms. GenAlEx was originally developed as a tool to assist us in our teaching of population genetic analysis, and is now widely used by university teachers and researchers around the world. In GenAlEx 6, we are pleased to introduce many new features for both teachers and researchers.

::DEVELOPER

GenAlEx Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX
  • Microsoft Excel(TM)

:: DOWNLOAD

GenAlEx

:: MORE INFORMATION

Citation

Peakall, R., Smouse, P.E., 2006.
GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research.
Molecular Ecology Notes 6, 288-295.

CONSRANK – Analysis,Comparison and Ranking of Docking Models based on Inter-residue Contacts

CONSRANK

:: DESCRIPTION

CONSRANK (CONSensus-RANKing) is a web service to easily and effectively analyse and rank docking models of protein-protein and protein-nucleic acid complexes, based on the frequency of inter-residue contacts.

::DEVELOPER

MoLNaC: Modeling Lab for Nanostructures and Catalysis 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts.
Chermak E, Petta A, Serra L, Vangone A, Scarano V, Cavallo L, Oliva R.
Bioinformatics. 2014 Dec 21. pii: btu837.

Cyber-T – Software and Server for Analysis of DNA Microarray data

Cyber-T

:: DESCRIPTION

Cyber-T is a a microarray analysis web interface from UCI’s Institute for Genomics and Bioinformatics. It accommodates both paired (2-dye) data and data in which control and experiment are on separate experiments (e.g. affymetrix based data). It also supports Bayesian statistical approaches and Bonferroni corrections for significance analysis of differentially expressed clones.

::DEVELOPER

Pierre Baldi and Tony Long at Institute for Genomics and Bioinformatics 

:: REQUIREMENTS

:: DOWNLOAD

 Cyber-T

:: MORE INFORMATION

Citation:

Kayala, M.A. and Baldi, P.,
“Cyber-T web server: differential analysis of high-throughput data“,
Nucleic Acids Research, 40 (W1): W553-W559, (2012).

P. Baldi and A.D. Long,
“A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Statistical Inferences of Gene Changes“,
Bioinformatics, 17, 6, 509-519, (2001).

TINGe 1.062 / GeNA 0.1 – Gene Networks Inference and Analysis

TINGe 1.062 / GeNA 0.1

:: DESCRIPTION

TINGe (Tool for Inferring Networks of GEnes) is a parallel and multi-platform framework for reconstructing gene regulatory networks from large gene expression data. It uses parallel processing, information theoretic criteria and statistical testing to derive networks with thousands of genes from microarray sets with thousands of observations. TINGe has been used to reconstruct a whole-genome network of Arabidopsis thaliana from 3,546 microarray measurements, which comprises of 15,495 genes.

GeNA (GEne Networks Analyzer) is a tool that for a given set of “seed” genes uses gene ranking mechanism to extract subnetworks of genes with similar biological function. GeNA uses algorithm akin to the topic-sensitive PageRank and it has been implemented as a stand-alone tool and as a plugin for Cytoscape.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TINGe / GeNA 

:: MORE INFORMATION

Citation:

Jaroslaw Zola, et al.
Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks
IEEE Transactions on Parallel and Distributed Systems. December 2010 (vol. 21 no. 12) pp. 1721-1733

WEBnm@ 3.3 – Web-server for Normal Mode Analysis of proteins

WEBnm@ 3.3

:: DESCRIPTION

WEBnm@ is meant to provide users with simple and automated computation and analysis of low-frequency normal modes for proteins.

::DEVELOPER

Reuter Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Dec 30;15(1):6597. [Epub ahead of print]
WEBnm@ v2.0: Web server and services for comparing protein flexibility.
Tiwari SP, Fuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N.

WEBnm@: a web application for normal mode analysis of proteins.
S.M.Hollup, G.Salensminde and N.Reuter.
BMC Bioinformatics (2005), 6(1): 52

SNPLINK – Multipoint Linkage analysis of Densely Distributed SNP data

SNPLINK

:: DESCRIPTION

SNPLINK is a Perl script that performs full genome linkage analysis of high-density single nucleotide polymorphism (SNP) marker sets. It first removes unlikely genotypes and performs parametric and non-parametric linkage analysis in a fully automated fashion. The presence of linkage disequilibrium (LD) between closely spaced SNP markers can falsely inflate linkage statistics. SNPLINK removes LD from the marker sets in an automated fashion and then carries out linkage analysis after LD has been removed. SNPLINK can compute both parametric and non-parametric statistics, utilising the freely available ALLEGRO and MERLIN software. Graphical outputs of whole genome multipoint linkage statistics are provided allowing comparison of results before and after the removal of LD

::DEVELOPER

Emily Webb, Professor Richard Houlston

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

SNPLINK

:: MORE INFORMATION

Citation

Webb et al. (2005)
SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.
Bioinformatics.21 (13): 3060-3061.

JMATING 1.0.8 – Analysis of Sexual Selection and Sexual Isolation Effects from Mating Frequency data

JMATING 1.0.8

:: DESCRIPTION

JMating allows to perform in an easy and intuitive way the most important sexual isolation and sexual selection estimates. Including the index of pair sexual isolation. It also allows for efficient bootstrapping of the estimators for testing hypothesis about sexual selection and isolation.

::DEVELOPER

Antonio Carvajal-Rodriguez 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows /MacOsX
  • Java 

:: DOWNLOAD

  JMating

:: MORE INFORMATION

Citation

Antonio Carvajal-Rodríguez and Emilio Rolán-Alvarez 2006.
JMATING: a software for the analysis of sexual selection and sexual isolation effects from mating frequency data.
BMC Evolutionary Biology 6:40

LTSOFT 3.0 – Analysis of Case-control Association Studies with known Risk Variants

LTSOFT 3.0

:: DESCRIPTION

LTSOFT is a software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender as well as genetic-covariates such as known associated variants when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power.

::DEVELOPER

Alkes Price

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LTSOFT

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jul 1;28(13):1729-37. doi: 10.1093/bioinformatics/bts259. Epub 2012 May 3.
Analysis of case-control association studies with known risk variants.
Zaitlen N, Pasaniuc B, Patterson N, Pollack S, Voight B, Groop L, Altshuler D, Henderson BE, Kolonel LN, Le Marchand L, Waters K, Haiman CA, Stranger BE, Dermitzakis ET, Kraft P, Price AL.

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