SnoopCGH Beta – Visualise and Explore Comparative Genomic Hybridization (CGH) data

SnoopCGH Beta

:: DESCRIPTION

SnoopCGH is a java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. The software allows the user to interactively analyse several sets of data simultaneously. The input is based on a tab-, space- or comma-delimited format, containing series of log intensity values corresponding to one or more comparisons or samples.

::DEVELOPER

PathogenSeq

:: SCREENSHOTS

:: REQUIREMENTS

Linux/windows /MacOsX
Java

:: DOWNLOAD

SnoopCGH

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Oct 15;25(20):2732-3. Epub 2009 Aug 16.
SnoopCGH: software for visualizing comparative genomic hybridization data.
Almagro-Garcia J, Manske M, Carret C, Campino S, Auburn S, Macinnis BL, Maslen G, Pain A, Newbold CI, Kwiatkowski DP, Clark TG.

GenomeCache 2.0.1 – Explore both McMillian Park and the realm of the Human Genome

GenomeCache 2.0.1

:: DESCRIPTION

Genome Cache was developed by the Educational Outreach Team at the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama. The original Genome Walk was created for McMillian Park, an outdoor area on the HudsonAlpha campus. The goal of Genome Cache? was to provide an engaging way for students and the public to explore both McMillian Park and the realm of the human genome.

::DEVELOPER

HudsonAlpha Institute for Biotechnology

:: SCREENSHOTS

:: REQUIREMENTS

iPad / iPhone

:: DOWNLOAD

GenomeCache

:: MORE INFORMATION

TempEst 1.5.3 – Explore Temporal Signal & Clocklikeness in Molecular Phylogenies

TempEst 1.5.3

:: DESCRIPTION

TempEst is a tool for investigating the temporal signal and ‘clocklikeness’ of molecular phylogenies. It can read and analyse contemporaneous trees (where all sequences have been collected at the same time) and dated-tip trees (where sequences have been collected at different dates). It is designed for analysing trees that have not been inferred under a molecular-clock assumption to see how valid this assumption may be. It can also root the tree at the position that is likely to be the most compatible with the assumption of the molecular clock.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Windows / Linux / MacOS

:: DOWNLOAD

TempEst

:: MORE INFORMATION

Citation

Virus Evol. 2016 Apr 9;2(1):vew007.
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen).
Rambaut A, Lam TT, Max Carvalho L, Pybus OG.

Voroprot 0.7.6.7 – Explore Geomeric Features of Protein Structure

Voroprot 0.7.6.7

:: DESCRIPTION

Voroprot is an interactive cross-platform software tool that provides a unique set of capabilities for exploring geomeric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

::REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

Voroprot

:: MORE INFORMATION

Citation

Kliment Olechnovič, Mindaugas Margelevičius and Česlovas Venclovas (2010)
Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.
Bioinformatics (2011) 27 (5): 723-724.

ForensicEA 1.0 / ForensicEALite 1.0 – Explore the Logic of Phylogeny Reconstruction

ForensicEA 1.0 / ForensicEALite 1.0

:: DESCRIPTION

ForensicEA / ForensicEALite lets the user explore the logic of phylogeny reconstruction. The program creates populations of virus particles. The populations evolve by genetic drift. The user can sample and complare nucleotide sequences from the populations. Various simulations let the user collect and analyze data on: genetic drift within a single population; divergence of populations by drift; and variation among populations on a known phylogeny.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows

:: DOWNLOAD

ForensicEA / ForensicEALite

:: MORE INFORMATION

EvoDots 1.1 – Explore the Mechanism of Evolution

EvoDots 1.1

:: DESCRIPTION

EvoDots lets the user explore the mechanism of evolution. The program creates a population of dots. The user is a predator. As the dots run around the screen, the user eats them by clicking on them with the mouse. After the user has eaten some of the dots, the survivors will reproduce. The population may or may note evolve, depending on the properties of the dots.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows

:: DOWNLOAD

EvoDots

:: MORE INFORMATION

GlobPlot / GlobPipe 2.3 – Explore Disorder or Globularity in Protein Sequences

GlobPlot / GlobPipe 2.3

:: DESCRIPTION

GlobPlot is a server for exploring disorder or globularity in protein sequences.GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N- or C-terminal segments that appear ordered.

GlobPipe is a pipeline that can be used for proteome scale analysis.

::DEVELOPER

Gibson Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
Biopython
TISEAN

:: DOWNLOAD

GlobPlot / GlobPipe

:: MORE INFORMATION

Citation

Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson
GlobPlot: exploring protein sequences for globularity and disorder
Nucleic Acid Res 2003 – Vol. 31, No.13

GenExp /DASgenexp – Web-based Visualization tool that interactively Explore Genomic Database

GenExp /DASgenexp

:: DESCRIPTION

GenExp is a web based and fully interactive visual DAS client. GenExp is a genome oriented DAS client capable of creating informative representations of genomic data zooming out from base level to complete chromosomes. It proposes a novel approach to genomic data rendering and uses the latest HTML5 web technologies to create the data representation inside the client browser.

DASGenExp is a web-based visualization tool that interactively explore distributed DAS data bases.

::DEVELOPER

the Algorithmics and Genetics Group

:: SCREENSHOTS

:: REQUIREMENTS

Firefox

:: DOWNLOAD

:: MORE INFORMATION

Citation

GenExp: an interactive web-based genomic DAS client with client-side data rendering.
Gel Moreno B, Messeguer Peypoch X.
PLoS One. 2011;6(7):e21270. Epub 2011 Jul 5.

Gene-warp 3.2 – Generate Alignment Matrices, Explore Temporal Asynchrony in Expression of Orthologs

Gene-warp 3.2

:: DESCRIPTION

Gene-warp is a tool to select ortholog pairs with best alignments and to explore alignment paths (not expression profiles!) shared by many genes. The program takes as an input two related datasets, containing profiles of orthologous genes.

::DEVELOPER

Dmitri Papatsenko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

Gene-warp

:: MORE INFORMATION

Citation

Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.

ExpressionView 1.00 – Explore Biclusters Identified in Gene Expression data

ExpressionView 1.00

:: DESCRIPTION

ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.

::DEVELOPER

Computational Biology Group ,Department of Medical Genetics, University of Lausanne

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX
R package

:: DOWNLOAD

ExpressionView

:: MORE INFORMATION

Citation

ExpressionView–an interactive viewer for modules identified in gene expression data.
Lüscher A, Csárdi G, de Lachapelle AM, Kutalik Z, Peter B, Bergmann S.
Bioinformatics. 2010 Aug 15;26(16):2062-3. Epub 2010 Jul 29.