MegAlign Pro Software for Multiple Sequence Alignments using MUSCLE, Mauve, or Clustal Omega


MegAlign Pro - Software for Multiple Sequence Alignments


Lasergene’s MegAlign Pro application enables you to easily perform multiple alignments of large DNA, RNA, or protein sequences using one of four alignment methods: MUSCLE, Mauve, MAFFT, or Clustal Omega. Profile alignment functionality additionally allows you to merge alignments or add sequences to an existing alignment. MegAlign Pro also offers several post-alignment analysis tools, including phylogenetic tree generation and access to a distance matrix, showing distances between each pair of sequences. MegAlign Pro's integrated views give you multiple ways to view your alignment simultaneously and several style options that allow you to control what's displayed. Color coding, rulers, and annotations (if available) can be used to assist you in locating variations and other items of interest. Following an alignment in MegAlign Pro, you can easily transfer your results to MegAlign where you can perform bootstrapping and generate additional reports. To learn more, see the Features or Resources tabs below.



Align Multiple Sequences with MUSCLE, Mauve, MAFFT, or Clustal Omega

  • Perform a multiple sequence alignment of large sequences using MUSCLE, Mauve, MAFFT, or Clustal Omega alignment methods
  • Concatenate a group of chromosomes, contigs, or fragments end-to-end to treat them as a single multi-segment sequence
  • Use the default alignment parameters or customize as needed
  • Check alignment quality using consensus match histogram

    Utilize Post-Alignment Analysis Tools

  • Generate phylogenetic trees to predict evolutionary relationships
  • Use the Distance Matrix to analyze distances between each pair of sequences
  • Explore sequence tracks to view GC content, gap fraction, sequence logos, and translation
  • For genomic alignments aligned with Mauve, explore the relationship between aligned blocks

    Easily Adjust the Interface to Meet Your Needs

  • Display/hide sequence annotations and features, and copy features to the consensus
  • Control the distance metric and phylogenetic tree layout
  • Utilize a variety of coloring and styling options for the best visual assessment of your alignment

    Export for Further Analysis

  • Export aligned sequences as FASTA (with gaps), MSF, GenBank, or Nexus files
  • Export phylogenetic tree or distance matrix
  • Integration with external tree viewer programs, such as FigTree
  • One-click export of alignment to MegAlign for additional analysis
  • Resources


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

    Technical Requirements

    Licensing Options


    Training Videos:

    »See all MegAlign Pro Videos

    »Or browse our full Video Library

    Product Literature:

    Quick-Start Installation Guide

    Lasergene Version Comparison Guide

    Lasergene Overview

    MegAlign Pro Online Help

    MegAlign Pro Tutorials

    Lasergene Tutorials

    Lasergene Tutorial Data - for Windows

    Lasergene Tutorial Data - for Macintosh

    For additional resources, please see our Support page.

    Try It

    Try MegAlign Pro 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

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    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.