MegAlign Multiple and Pairwise Sequence Alignment Software


Software for Multiple and Pairwise Sequence Alignments


DNASTAR'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.

In addition to MegAlign, Lasergene Molecular Biology Suite also offers MegAlign Pro for performing large multiple alignments using MUSCLE, Mauve, MAFFT, or Clustal Omega.


MegAlign Multiple and Pairwise Sequence Alignment Software

Features & Highlights


Align Sequences

  • Choose from many popular DNA and protein sequence alignment methods: Clustal, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson or DotPlot.
  • Easily create sub alignments by selecting ranges of longer alignments to create neat blocks of similarity, or to remove ‘ragged’ termini resulting from inconsistent sequence data length.
  • Download sequences directly from NCBI or a database using accession numbers, BLAST, or text searches to match the highlighted segment of your current sequence. If desired, add search results to the alignment project.

MegAlign Calmodulin Sequence Alignment


MegAlign Sequence Alignment Report

Discover Evolutionary Relationships

  • View calculations of sequence similarity and distance in relation to the constructed phylogeny.
  • Customize alignment results by inserting or moving gaps, or by highlighting residues that match/mismatch the consensus sequence or constituent sequences.
  • Define a custom consensus by residue or by chemical, structural, or charge characteristics.
  • Display consensus strength as a color-coded histogram.
  • Use bootstrapping to test for consistency and robustness of trees created using one of the Clustal methods.