BetaMol v0.92d – Molecular Modeling, Analysis, and Processing software

BetaMol v0.92d

:: DESCRIPTION

BetaMol is a molecular modeling, analysis, and processing software completely based on the theory of the Voronoi diagram, the quasi-triangulation, and the Beta-complex.

::DEVELOPER

Voronoi Diagram Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BetaMol

:: MORE INFORMATION

Citation

Youngsong Cho, Jae-Kwan Kim, Joonghyun Ryu, Chung-In Won, Chong-Min Kim, Donguk Kim, and Deok-Soo Kim,
BetaMol: a molecular modeling, analysis and visualization software based on the beta-complex and the quasi-triangulation,
Journal of Advanced Mechanical Design, Systems, and Manufacturing, Vol.6, Issue 3, pp. 389-403, 2012

WebLab 1.2 – Multifunctional Bioinformatics Analysis Platform

WebLab 1.2

:: DESCRIPTION

WebLab is a multifunctional bioinformatics analysis platform integrating diversified tools with unified, user-friendly web interface. However, WebLab is not a mere bioinformatics toolbox, we also offer powerful data management function, group strategy and knowledge sharing mechanism, which will bring considerable advance of efficiency for both wet bench and in silico scientists working in biomedicine community.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 WebLab

:: MORE INFORMATION

Citation

Liu, X., Wu, J., Wang, J., Liu, X., Zhao, S., Li, Z., Kong, L., Gu, X., Luo, J. and Gao, G. (2009)
WebLab: a data-centric, knowledge-sharing bioinformatic platform.
Nucleic Acids Res.2009) doi: 10.1093/nar/gkp428

analysis 0.8.8 – Evolutionary Genetic Analysis

analysis 0.8.8

:: DESCRIPTION

analysis – C++ software for evolutionary genetic analysis.

::DEVELOPER

Thornton Lab at UC Irvine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 analysis

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Nov 22;19(17):2325-7.
Libsequence: a C++ class library for evolutionary genetic analysis.
Kevin Thornton

GenePath – Analysis of Genetic Data and Discovery of Genetic Networks

GenePath

:: DESCRIPTION

GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks.

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

:: REQUIREMENTS

  • Any Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

GenePath: from mutations to genetic networks and back.
Juvan P, Demsar J, Shaulsky G, Zupan B.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W749-52.

dictyExpress 1.5 – Dictyostelium Gene Expression Analysis

dictyExpress 1.5

:: DESCRIPTION

dictyExpress is an interactive, web-based exploratory data analytics application providing access to over 1,000 Dictyostelium gene expression experiments from Baylor College of Medicine. The applications consists of components for data retrieval, selection of individual genes or groups of genes, graphic display of gene expression time courses, Gene Ontology term enrichment analysis, display of gene co-expression networks, hierarchical clustering, and expression profile visualization of selected genes in different experiments. The components are connected such that a change in any one of the components (e.g., selection of a gene subset from the hierarchical clustering dendrogram) can propagate to other components and their associated visualizations.

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

:: REQUIREMENTS

  • Any Web Browser

:: DOWNLOAD

 dictyExpress

:: MORE INFORMATION

Citation:

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface.
Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B.
BMC Bioinformatics. 2009 Aug 25;10:265.

ReadXplorer 2.2.3 – Visualization and Analysis of Mapped Sequences

ReadXplorer 2.2.3

:: DESCRIPTION

ReadXplorer is a freely available comprehensive exploration and evaluation tool for NGS data. It extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ReadXplorer

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 30. [Epub ahead of print]
ReadXplorer – Visualization and Analysis of Mapped Sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A.

draw+sneakpeek – DNA Resequencing Analysis Workflow

draw+sneakpeek

:: DESCRIPTION

DRAW and SneakPeek are two computer programs that we use for analyzing whole-genome and whole-exome DNA-seq experiments.

DRAW stands for DNA Resequencing Analysis Workflow. DRAW automates the entire process of mapping sequence reads, various quality control steps and calling variants.

SneakPeek is a web-based diagnostic tool for reviewing quality metrics generated by our DNA Resequencing Analysis Workflow (DRAW).

::DEVELOPER

 Wang Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Amazon EC2 / Linux

:: DOWNLOAD

 draw+sneakpeek

:: MORE INFORMATION

Citation

Lin CF, Valladares O, Childress DM, Klevak E, Geller ET, Hwang YC, Tsai EA, Schellenberg GD, and Wang LS.
DRAW+SneakPeek: Analysis Workflow and Quality Metric Man-agement for DNA-Seq Experiments.
Bioinformatics (2013) 29 (19): 2498-2500. doi: 10.1093/bioinformatics/btt422

SNiPlay v3 – SNP and Polymorphism Analysis

SNiPlay v3

:: DESCRIPTION

SNiPlay is a web-based tool for SNP and polymorphism analysis.From sequencing traces, alignment or allelic data given as input, it detects SNP and insertion/deletion events.

::DEVELOPER

SNiPlay team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.
Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard JF, Ruiz M.
Nucleic Acids Res. 2015 Jun 3. pii: gkv351.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.
Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

MIDAS 1.0 – Analysis and Visualisation of Interallelic Disequilibrium between Multiallelic Markers

MIDAS 1.0

:: DESCRIPTION

MIDAS (Multiallelic Interallelic Disequilibrium Analysis Software) is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers.

::DEVELOPER

Tom Gaunt’s group in the MRC IEU

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Mac OsX / Windows
  • Python

:: DOWNLOAD

 MIDAS

:: MORE INFORMATION

Citation:

Tom R Gaunt, Santiago Rodriguez, Carlos Zapata, Ian NM Day
MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers.
BMC Bioinformatics 2006, 7:227 (27 April 2006)

dChip 2011.12 – Analysis & Visualization of Gene Expression & SNP Microarrays

dChip 2011.12

:: DESCRIPTION

DNA-Chip Analyzer (dChip) is a Windows software package for probe-level (e.g. Affymetrix platform) and high-level analysis of gene expression microarrays and SNP microarrays.

Gene expression or SNP data from various microarray platforms can also be analyzed by importing as external dataset. At the probe level, dChip can display and normalize the CEL files, and the model-based approach allows pooling information across multiple arrays and automatic probe selection to handle cross-hybridization and image contamination. High-level analysis in dChip includes comparing samples, hierarchical clustering, view expression and SNP data along chromosome, LOH and copy number analysis of SNP arrays, and linkage analysis. In these functions the gene information and sample information are correlated with the analysis results.

::DEVELOPER

Started in Wing Wong Lab , Developed & Maintained by Cheng Li Lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Linux with Wine
  • Mac with Virtual PC

:: DOWNLOAD

dChip

:: MORE INFORMATION

Please cite Li and Wong 2001a if dChip results are used in manuscripts, and cite Lin et al. 2004 if dChip SNP analysis functions are used.