Download OmicsBox

Download OmicsBox

Download here the latest version of OmicsBox for free (on the right). The download contains an executable installer which will install OmicsBox on your computer. Choose between Windows, Mac or Linux based versions. No need to install Java.

How do I get an activation key?

Just click here and register with your name and email and we will send you your key immediately. Registration takes less than 1 minute.

System Requirements

OmicsBox is available for Mac (10.9+), Windows (7+) and Linux systems (Ubuntu 14.14+, Debian 8+, RedHat Enterprise Linux 7). The Linux systems require > gtk2-2.24. We recommend at least 2GB of RAM. A working internet connection is required to use many of the application features.OmicsBox supports automatic updates (write permissions required).

Release History and Versions

  • Blast2GO is now OmicsBox
  • General
    • Search box for menu actions
    • Improved citations in wizards and reports
    • New menu structured by modules
    • Bug fixes and improvements
  • Functional Annotation
    • New CloudBlast taxonomy filtering
    • Improved CloudIPS speed and resource usage
    • New EC class (7)
  • Genome Analysis
    • DNA-Seq De Novo Assembly (ABySS 2.0)
    • Repeat Masking (RepeatMasker)
  • Transcriptomics
    • RNA-Seq Alignment against reference genome (STAR)
  • New Module: Metagenomics
    • Taxonomic Classification (Kraken)
    • Metagenomic Assembly (MEGAHIT and meta-SPAdes)
    • Metagenomic Gene Prediction (FragGeneScan and Prodigal)
  • Fix to prevent B2G files from becoming corrupted
  • Improve GFF export functions
  • Improve error handling on truncated GFF input
  • Fix Extract Fasta from GFF feature hierarchy
  • Improve GFF/GTF attribute detection
  • Improve GTF gene structure visualization
  • Fix KEGG objects save issue
  • Improve GSEA memory handling
  • Improve Workflows inputs/outputs handling
  • Improve Generic Statistics side-panel
  • Load TimeLogic file parsing improvements
  • Minor Fixes
  • Import Blast Results: minor bug fixes
  • Workflows: minor bug fixes and improvements
  • Kegg: memory optimizations
  • GO Graphs: memory optimizations when exporting png
  • InterProScan: improve progress communication
  • NCBI Blast: improve communication in case of errors
  • Create Count Table: memory and performance optimizations
  • Venn Diagrams
  • FastQ Pre-Processing (Adapters, Quality, Length)
  • Workflows allow regular files as input and output
  • Context Menu for GFF and VCF tables
  • GSEA with “No Filter” option
  • Minor bug fixes and improvements
  • Improved Sequence Viewer
  • Genome Browser performance improvements
  • RNA-Seq De-Novo Assembly report improvements
  • Changed colors for up(red)/down(green) regulated pairwise statistics
  • KEGG with https connection
  • Rfam connection improvements
  • Minor bug fixes and improvements
  • FastQ Quality Check
  • RNA-Seq DeNovo Assembly
  • Combined Genome Browser Visualization
  • Support for Variant Call Format
  • Merge Blast2GO Projects using the File Manager
  • Interactive Heatmap from Pairwise Results
  • Network License Support
  • InterProScan in the Cloud (CloudIPS)
  • Workflows (Create, View, Run)
  • De-Novo Transcript Level Quantification (Fasta + FastQ)
  • Blast Result Alignment Viewer
  • High Performance GFF File Viewer
  • PDF Reports for “RNA-Seq” and “Gene Finding” features
  • New Gene Ontology ID-Mapping Strategy (faster, more complete, “gi” independent)
  • New design for many result pages
  • “Find Similar Sequences” performance improvements
  • Faster Species Taxonomy Queries
  • Preferences: Define Memory and Temporary Files Settings
  • Preferences: Choose Gene Ontology Version: latest or month
  • Improved “Cloud Usage” Monitor
  • CloudBlast now for multiple Projects in parallel
  • Prokaryotic GeneFinding (Glimmer): Improved Perform. and Report
  • GO Graph Visualisation: Improved Filtering
  • InterProScan: Improved Communication
  • Rfam: Merge GOs to Projects
  • BioMart: More Stable Data Retrieval
  • Minor Bug Fixes
  • RNAseq Read Count to Quantify Expression (BAM + GFF)
  • Coding Potential Assessment (CPAT)
  • New Result Table (side-panel, tags, colors, filters, context menu)
  • Enrichment analysis now for ANY functional label
  • Differential Expression Analysis with improved visualisations
  • Faster Gene Finding
  • Memory and CPU Monitor
  • Improved “Extract Fasta” feature (GFF + Ref-Fasta)
  • Improved GFF table to easily search and filter attributes
  • Gene Finding: RNA-Seq Exon Support for Augustus
  • Differential Expression Count Table: Improved format check
  • GSEA enriched GO Gene-List export feature
  • NCBI Blast: Improved application messages
  • File Manager: Improved performance
  • Minor Bug Fixes
  • Differential Expression Analysis for Pairwise and TimeCourse
  • Gene Finding for Eukaryotes and Prokaryotes
  • Gene Set Enrichment Analysis (GSEA)
  • ID and Sequences Conversion by: Extract Top Hit Sequences via Blast and Blat
  • New App Manager now with Blast2GO “Featured” Apps
  • Blast2GO Featured App: Create NCBI Submission Files
  • New App: Ortholog Group Finder (COG/EggNOG)
  • New Load and Export Functions: CountTable, GFF3 Object, ID-Value List, Generic Table
  • New Organic Graph Layout
  • Generic Table Column have now a (Un)Select All function
  • We added Icons to the Load, Export and Context Menu
  • Improved QBlast and Local Blast (now version 2.4) behaviour
  • Improved Proxy Settings (now available via the activation dialog)
  • Fixed InterProScan Bug with ORF prediction
  • New BASIC feature: Easily create and blast against a local databases.
  • New filters can be applied during the annotation step. These filters allow e.g. to easily perform a “Top-Hit-with-GOs” annotation.
  • New feedback forms allows us to improve Blast2GO with the help of your input.
  • The new Blast2GO App Manager allows to add additional tools to Blast2GO.
  • Predict bacterial protein subcellular localization annotations with PSORTb 3.
  • The “Translate longest ORF” feature has now many more options and allows you to choose the open reading frame based on the Top Blast Hit.
  • Create distribution charts (dot, bar, line) of any of your generic table columns.
  • Easily find and remove highly similar and/or redundant sequences within large datasets using the BLAT algorithm.
  • Faster Gene Ontology Mapping in BASIC mode via web services (no direct mysql connection with an open network port 3306 needed).
  • New interactive offline Gene Ontology graph visualisation.
  • Blast results in new XML2 format for improved Gene Ontology Mapping and taxonomy information.
  • Analysis history for all Blast2GO files.
  • Improved Gene Ontology import for gene symbol, accession and GenBank ID lists.
  • Improved InterProScan XML import.
  • Merge Blast2GO datasets direclty from within the FileManager.
  • Top Blast Hit export now available in the Generic Export function.
  • Several new summary charts for the Gene Ontology Mapping and the InterPro step.
  • Work with multiple datasets in paralell (PRO feature).
  • Use the FileManager to organize your datasets and results.
  • Save and reopen all analysis results like graphs, charts, enrichments, etc.
  • Run RFAM analysis. Detect non-coding RNA, cis-regulatory elements or self-splicing RNAs (via EMBL-EBI webservice).
  • WordCloud or Treemap viewer allow to summarize functional profiles.
  • Extract FASTA sequences via GFF/GTF files.
  • Extract subsets and ID list from your project.
  • Customize your sequence table columns (e.g. remove columns you are not interested in).
  • A new Fast-Blast option to speed-up your blast results.
  • Blast2GO in a fresh new look.
  • Many performance, design and user interface aspects have been improved.
  • Progress bars, application messages and many other tools make working with Blast2GO now more efficient.
  • Last release of the Blast2GO Java WebStart version.
  • The development and maintenance/update of this version is now discontinued.

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Blast2GO is now part of OmicsBox.
If you are interested in a Blast2GO Subscription please see:
OmicsBox – Functional Analysis Module  

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Blast2GO is now part of OmicsBox