MegAlign Software for Multiple and Pairwise Sequence Alignments

MegAlign - Software for DNA and Protein Sequence Alignments and Analysis


Lasergene’s MegAlign is sequence alignment software offering both DNA and protein sequence alignment using a range of pairwise and multiple alignment methods. Rich graphical displays allow you to adjust your finished alignment, as well as analyze phylogeny, differences in chemical, structural, or functional characteristics. MegAlign is fully integrated with GenVision, allowing for the creation of publication-quality images of your alignments. To learn more, see the Features or Resources tab below.


"MegAlign is very intuitive and easy to use, and the results are instantaneous."

Ines Santisteban, Duke University


Align Sequences

  • Align DNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including Clustal, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis. 
  • Easily create sub alignments by selecting ranges of longer alignments to create neat blocks of similarity or to remove the ‘ragged’ termini due to length variance in your data.
  • Download sequences directly from NCBI or a database using accession numbers, BLAST, or text searches to match the highlighted segment of your current sequence or to add a search result to your current project.


  • View evolutionary relationships predicted from your multiple sequence alignment. The length of each pair of branches represents the distance between sequence pairs, while the units at the bottom of the tree indicate the number of substitution events. 
  • Use the Bootstrapping method to test for consistency and robustness of a tree created using a Clustal methodology. The branch patterns with higher values are statistically more likely to occur, and give a measure of confidence in the optimal tree structure.Video See it!
  • Calculate sequence similarity and distance in relation to the constructed phylogeny.

    Analyze Alignment Results

  • Edit or adjust your finished alignment by inserting or moving gaps.
  • Customize your alignment results by highlighting residues that match/mismatch the consensus, or other sequences in the project.  Define a custom consensus by residue or by chemical, structural, or charge characteristics and display the consensus strength as a color-coded histogram. Video See it!
  • Export your alignments into several popular formats. Or, export your alignment as a GenVision project for creation of publication-quality images. Video See it!
  • Resources


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

    Technical Requirements

    Licensing Options


    Training Videos:

    »See all MegAlign Videos

    »Or browse our full Video Library

    Product Literature:

    Quick-Start Installation Guide

    Lasergene Version Comparison Guide

    Lasergene Overview

    MegAlign Tutorials

    All Lasergene Tutorials

    MegAlign Online Help

    Lasergene Tutorial Data - for Windows

    Lasergene Tutorial Data - for Macintosh

    For additional resources, please see our Support page.

    Try It

    Try MegAlign 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.