Sibelia 3.0.7 – Synteny Block ExpLoration tool

Sibelia 3.0.7 / C-Sibelia

:: DESCRIPTION

Sibelia is a comparative genomic tool。 It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments.

C-Sibelia is a highly accurate and easy-to-use software tool for comparing two closely related bacterial genomes, which can be presented as either finished sequences or fragmented assemblies.

::DEVELOPER

Algorithmic Biology Lab at St. Petersburg Academic University of the Russian Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows

:: DOWNLOAD

 Sibelia

:: MORE INFORMATION

Citation

F1000Res. 2013 Nov 25;2:258. doi: 10.12688/f1000research.2-258.v1. eCollection 2013.
C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison.
Minkin I, Pham H, Starostina E, Vyahhi N, Pham S

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham.
Sibelia: A fast synteny blocks generation tool for many closely related microbial genomes
(submitted)

ChAsE 1.0.11 – Chromatin analysis and exploration tool

ChAsE 1.0.11

:: DESCRIPTION

ChAsE is a cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments.

::DEVELOPER

ChAsE team

:: SCREENSHOTS

ChAsE

:: REQUIREMENTS

  • Windows/Mac OsX/ Linux
  • Java

:: DOWNLOAD

 ChAsE

:: MORE INFORMATION

Citation

ChAsE: Chromatin analysis and exploration tool.
Younesy H, Nielsen CB, Lorincz MC, Jones SJ, Karimi MM, Möller T.
Bioinformatics. 2016 Jul 4. pii: btw382.

ETE 3 – Python Environment for Phylogenetic Tree Exploration

ETE 3

:: 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  in the Centre for Genomic Regulation (Barcelona, Spain).

:: 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 Price lab at ISB

:: 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.

CummeRbund 2.10.0 – Exploration, Analysis and Visualization of Cufflinks high-throughput RNA-Seq data

CummeRbund 2.10.0

:: DESCRIPTION

CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.CummeRbund was designed to help simplify the analysis and exploration portion of RNA-Seq data derrived from the output of a differential expression analysis using cuffdiff with the goal of providing fast and intuitive access to your results.

::DEVELOPER

the Computational Biology group &  the Rinn Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 CummeRbund

:: MORE INFORMATION

Citation

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016.
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

sMOL Explorer 1.1 – Database and Exploration tool for Small MOLecules datasets

sMOL Explorer 1.1

:: DESCRIPTION

sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction, and statistical analysis and data mining through Web interface. With sMOL Explorer, users can create his/her own database by adding each small molecule via a drawing interface or uploading the data files from internal and external projects into the sMOL database. Then, the database can be browsed and queried with textual and structural similarity search. The molecule can also be submitted to search against external public databases including PubChem, KEGG, DrugBank and eMolecules. Moreover, users can easily access a variety of data mining tools to perform analysis including (1) finding the frequent substructure, (2) clustering the molecular fingerprints, (3) identifying and removing irrelevant attributes from the data, and (4) building the classification model of biological activity.

::DEVELOPER

Information Systems Laboratory at BIOTEC

:: SCREENSHOTS

sMOLExplorer

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

sMOL Explorer

:: MORE INFORMATION

CitationBioinformatics. 2007 Sep 15;23(18):2498-500. Epub 2007 Jul 27.
sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets.
Ingsriswang S1, Pacharawongsakda E.

Elviz – Exploration of Metagenomic Assemblies

Elviz

:: DESCRIPTION

Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenome data and their complex metadata.

:: DEVELOPER

Joint Genome Institute (JGI).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web  browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Elviz – exploration of metagenome assemblies with an interactive visualization tool.
Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I.
BMC Bioinformatics. 2015 Apr 28;16(1):130.

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.

imDEV 1.4.2 – omics data exploration and visualization in Excel

imDEV 1.4.2

:: DESCRIPTION

imDEV (Interactive modules for Data Exploration and Visualization) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enable interactive and dynamic analyses of large data by interfacing R’s multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal (PCA) and independent component analyses (ICA), partial least squares regression (PLS) and discriminant analysis (PLS-DA), through an intuitive interface for creating high quality two and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and  correlation networks.

::DEVELOPER

Dmitry Grapov

:: SCREENSHOTS

imDEV

:: REQUIREMENTS

  •  Excel
  • R package

:: DOWNLOAD

 imDEV

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2288-90. doi: 10.1093/bioinformatics/bts439. Epub 2012 Jul 18.
imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel.
Grapov D, Newman JW.

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 at The Institute of Evolutionary Biology University of Edinburgh

:: 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.