Tag: Exploration

Badger 1.1 – An Accessible Genome Exploration Environment

Badger 1.1

:: DESCRIPTION

Badger provides an easy to use and intuitive way to explore and store genome data and gene predictions. It can be used as a central hub for genome projects allowing project members to search and access data as and when it is available. The database can hold multiple species, each with multiple genome versions and each genome with multiple gene prediction sets.

::DEVELOPER

The Blaxter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Badger

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2788-9. doi: 10.1093/bioinformatics/btt466. Epub 2013 Aug 11.
Badger–an accessible genome exploration environment.
Elsworth B1, Jones M, Blaxter M.

 

Cobweb 1.1.1 – Network Exploration and Visualisation

Cobweb 1.1.1

:: DESCRIPTION

Cobweb is a Java applet for real-time network visualization; its strength lies in enabling the interactive exploration of networks.

::DEVELOPER

Structural Bioinformatics Group

:: SCREENSHOTS

Cobweb

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Cobweb

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1725-6. doi: 10.1093/bioinformatics/btr195. Epub 2011 Apr 12.
Cobweb: a Java applet for network exploration and visualisation.
von Eichborn J1, Bourne PE, Preissner R.

ETE 3.1.1 – Python Environment for Phylogenetic Tree Exploration

ETE 3.1.1

:: DESCRIPTION

ETE (Environment for Tree Exploration ) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic and other type of trees. It provides a wide range of tree handling methods, node annotation features, programmatic access to the phylomeDB database, and automatic orthology and paralogy prediction methods. In addition, an interactive tree visualization program, as well as a highly customizable tree drawing engine, is included.

::DEVELOPER

Gabaldón’s lab

:: SCREENSHOTS

N/A

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ETE

:: MORE INFORMATION

Citation:

ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas J, Serra F, Bork P.
Mol Biol Evol. 2016 Feb 26. pii: msw046.

Jaime Huerta-Cepas*, Joaquín Dopazo and Toni Gabaldón*.
ETE: a python Environment for Tree Exploration.
BMC Bioinformatics 2010, 11:24.

ITEP 1.1 – Integrated Toolkit for Exploration of Pan-genomes

ITEP 1.1

:: DESCRIPTION

ITEP is a suite of scripts and Python libraries for the comparison of microbial genomes. It includes tools for de novo protein family prediction by clustering, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, cluster curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Python

:: DOWNLOAD

 ITEP

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jan 3;15:8. doi: 10.1186/1471-2164-15-8.
ITEP: an integrated toolkit for exploration of microbial pan-genomes.
Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND1.

MSMS 3.2rcb122 / MSMSPlay – Coalescent Simlation tool with Selection / Exploration of Basic Population Genetic Theory

MSMS 1.3 / MSMSPlay

:: DESCRIPTION

MSMS is a coalescent simulator that models itself off Hudsons ms in usage and includes selection. It is fast, often faster than ms, and portable running on Mac OSX, windows and Linux. By using this tool, one can study the patterns of selection in complicated demographic scenarios.

MSMSPlay is a GUI designed for simple exploration of basic population genetic theory. Its meant for exploratory runs with some useful output in an interactive fashion.

::DEVELOPER

The Mathematics and BioSciences Group

:: SCREENSHOTS

MSMSPlay

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 MSMS / MSMSPlay

:: MORE INFORMATION

Citation

Ewing G. and Hermisson J. (2010).
MSMS: A coalescent simulation program including recombination, demographic structure, and selection at a single locus.
Bioinformatics 26: 2064-2065.

RNA2DMap v2 – Visual Exploration of RNA Structure

RNA2DMap v2

:: DESCRIPTION

RNA2DMap is a structural interface to comparative data. Currently, RNA2DMap presents three-dimensional RNA distances, tertiary interactions, conservation values, motifs, basepair groups, basepair conformations and coaxial stacks on interactive secondary structure models.

::DEVELOPER

the Gutell Lab

:: SCREENSHOTS

RNA2DMap

:: REQUIREMENTS

:: DOWNLOAD

 RNA2DMap

:: MORE INFORMATION

Citation

Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011)
RNA2DMap: A Visual Exploration Tool of the Information in RNA’s Higher-Order Structure.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA.

EpiExplorer – Exploration and Analysis of large Epigenomic Datasets

EpiExplorer

:: DESCRIPTION

EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing.

::DEVELOPER

the Computational Epigenetics Group at the Max-Planck Institute for Informatics.

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer and Christoph Bock
EpiExplorer: live exploration and global analysis of large epigenomic datasets
Genome Biology 2012, 13:R96

GLIEP – Navigation and Exploration of Interconnected Pathway Visualization

GLIEP

:: DESCRIPTION

GLIEP (Glyph-based Link Exploration of Pathways) helps to guide the navigation and exploration process of interconnected pathway visualization as well as providing insight into the overall interconnectivity.

::DEVELOPER

The ISOVIS group

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GLIEP

:: MORE INFORMATION

Citation

I. Jusufi, C. Klukas, A. Kerren, and F. Schreiber
Guiding the Interactive Exploration of Metabolic Pathway Interconnections
In Information Visualization, 2011. SAGE Publications

MuGeN 20060919 – Exploration of Multiple Annotated Genome Portions

MuGeN 20060919

:: DESCRIPTION

MuGeN (Multi-Genome Navigator) is an interactive tool enabling exploration in several annotated genomes completed by results of in silico analysis. It can also run in batch mode enabling it to generate images of various formats. This operating mode means that it can be integrated into Websites for displaying annotated physical maps. MuGeN is listed on the FreshMeat and Bioinformatics.Org portals.
Mark Hoebeke

::DEVELOPER

Mark Hoebeke

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MuGeN

:: MORE INFORMATION

Citation

M. Hoebeke, P. Nicolas and P.
MuGeN: simultaneous exploration of multiple genomes and computer analysis results
Bioinformatics (2003) 19 (7): 859-864