SeqNinja - Powerful Sequence Editing Software, Batch Sequencing Editing, Batch Sequence Annotation

SeqNinja - Software for Automated Editing of Genome Sequences and Annotations


SeqNinja is a convenient tool for automated and batch editing of genome sequences and annotations. SeqNinja makes it easy for you to convert file formats, batch edit and export annotations, merge and split sequence data, and transfer annotations between genome versions, automating the process of adjusting sequence coordinates between assemblies. SeqNinja provides you with a variety of templates for common functions, as well as the ability to infinitely customize your projects. To learn more, see the Features or Resources tab below.


Video SeqNinja Overview Video


Powerful Toolkit for Automated Genome Editing

  • Following a de novo assembly, use SeqNinja to concatenate the generated contigs for ease of use in downstream analysis.
  • Easily make corrections to large sequences by inserting or substituting bases while SeqNinja adjusts annotation coordinates automatically.
  • Circularly permute a sequence within a gene of interest such that it is linearized at a different location.
  • Maintain a history of sequence edits within each sequence file.

    Streamlined Processing of Large Sequence Data Sets

  • Generate a multi-sequence FASTA file by extracting features, generating a reverse complement of your sequences, or translating a GenBank file.
  • Create custom sequence sets based  on sequence names or patterns, and then use the resulting sets as the source for downstream operations such as feature extractions.
  • Sample sequences at random or based on user-defined criteria from large, multi-sequence files.
  • Use MegAlign Pro to run SeqNinja scripts and align resulting sequences directly.

    Flexible Graphical User Interface

  • Organize modules to create a custom program for your project
  • Use a variety of input file types for your projects, including FASTA files, GenBank files, and DNASTAR Lasergene files, and quickly convert between these formats.
  • Create your program in visual or text views, for both beginning and advanced SeqNinja users.





    Whether you are a long time customer, or are just starting to learn about SeqNinja, you may find some of the following resources helpful:

    Technical Requirements

    Licensing Options


    Product Literature:

    Quick-Start Installation Guide

    SeqNinja User's Guide

    Lasergene Version Comparison Guide

    Lasergene Overview

    SeqNinja Tutorials

    All Lasergene Tutorials

    SeqNinja Online Help

    SeqNinja Online Help (Command-Line Version)

    Lasergene Tutorial Data - for Windows

    Lasergene Tutorial Data - for Macintosh

    For additional resources, please see our Support page.

    Try It

    Try SeqNinja for Free!

    Request a fully functional free trial of DNASTAR Lasergene to try it out for yourself.


    Free Trial for Windows

    Free Trial for Macintosh

    Buy It

    Ready to Buy?

    To purchase DNASTAR Lasergene, please fill out our brief quote request form. A member of our dedicated sales team will respond to you within one business day.