Blast2GO Command Line Tools

A Functional Annotation Pipeline

The Blast2GO Command Line is a professional solution for flexible, high-performance and automatic functional annotation tasks. This Annotation Pipeline allows you to integrate and automate your functional annotation task in a flexible way. Generate high-quality results in a reproducible way directly integrated into your data analysis workflows.

High Performance

The command-line version of Blast2GO allows you to analyse large dataset on your performant computing servers will nearly no extra effort.


Easily integrate your functional annotation tasks within your custom analysis pipeline and run different analysis scenarios in parallel.

Automatic Data Generation

Generate all the statistics charts Blast2GO offers in an automatic fashion. This includes a summary report in PDF as well as images and text file formats.


Control the whole analysis with a simple configuration file. This allows you to set up different analysis strategies and reproduce the multiple scenarios for one or various datasets.


Run BLAST, InterProScan and the Blast2GO annotation offline on your own servers according to your security requirements. Take 100% control of data sources and versions you use throughout the analysis.

Obtain a download link and instructions on how-to try a full-functional Blast2GO Command Line version directly via email. 

Total price: 0 €
Without taxes

Licensing Options

Several options are available to license the Blast2GO CommandLine depending on your setup scenario.

  • Single Server License: This static licence allows to install the CommandLine on one server/workstation. No paralell executions are allowed. To request a trial license please fill this form .
  • Floating Network License: This licence allows to run the CommandLine on a specified, flexible number of server within your organization via a Network License Server. Paralell executions are possible. MultiFor more information please write to: sales@biobam.com

System Requirements

  • Blast2GO Command line tools are designed to work on all three major platforms (Linux, Mac OS, Win).
  • All systems have to have Java 11+ installed.
  • We recommend at least 1 GB of ram.
  • For a local Blast2GO database a MongoDB server (version 3.4.6+) is necessary.

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Main Features

Run Blast2GO on your own servers and control all analysis steps from the command line.

  • Automate your functional annotation
  • Reproduce your results in a consistent manner
  • Design advanced annotation strategies
  • Integrate Blast2GO into your existing analysis pipeline
  • Generate comprehensive PDF reports (see example report: Tomato)
  • Save all your results to specific project folders
  • Work consistent and effective once you found the right settings for your analysis. The Command Line offers a very detailed and explicatory property file
  • Run Blast locally or via Blast2GO CloudBlast
  • Run a remote InterProScan directly from within the Blast2GO command line
  • Extract Fasta sequences from a Reference Genome via a GFF or GTF file
  • Work offline. The Command Line supports easy Blast2GO database installation and updates
  • More detailed logging, additional export functions, etc …

Software Versions

  • Fixed InterProScan parsing issue with certain XML tags
  • Fixed analysis report
  • Removed GO Mapping database chart
  • Now requires Java 11
  • Added Cloud InterProScan
  • Fix: Possible file corruption bug
  • Fix: Applied bug fix to allow annotation of unconventional Blast hits
  • Update: Enzyme resource files
  • Update: GO Dag OBO file
  • Update: Taxonomy info files
  • Fix: Report failed because of erroneous enzyme commission codes
  • Update: Enzyme resource files
  • Update: GO Dag OBO file
  • Fix: license.lic not found on CentOS
  • Fix: Reprise libraries now in temporary folder
  • New GO Mapping now based on MongoDB
  • Adaption of CloudBlast to the new BioBam Cloud Platform
  • New Generic Export Function allows extensive customized CSV data export
  • Annotation Export includes now Enzyme Codes
  • Additional parameters for the Longest ORF function
  • Improved file handling allows relative file paths, white spaces in file names and automatic file extensions
  • Fixed Export SeqTable function (duplicated description line)
  • New licensing system that allows for floating licenses (e.g. clusters or multiple workstations)
  • New -ecmapping switch to retrieve Enzyme Codes from annotated GOs (Included in -annotate step)
  • Minor bug fixes
  • Gene Ontology mapping and overall speed improvements
  • Option to specify a location to store all temporary files with the parameter -tempfolder
  • New statistic charts for GO mapping, Enzyme Codes and InterProScan results added
  • Gene Ontology Graph visualization has been removed
  • Fixed compatibility issue of .b2g files generated with the Blast2GO Desktop version
  • Fix for headless environments (systems without any graphics support)
  • Bug fix for InterProScan import function
  • Allows a non standard port for the local database connection
  • Improved PDF report (see attached example: Tomato)
  • Run Blast locally or via the Blast2GO CloudBlast
  • Run a remote InterProScan directly from within the Blast2GO command line
  • Improved local database installation and update
  • Extract Fasta sequences from a Reference Genome via a GFF or GTF file
  • More detailed and explicatory properties file
  • More detailed logging and additional export functions