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 and offers four alignment methods: MUSCLE, Mauve, MAFFT, and 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 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.


Features & Highlights


Align Multiple Sequences

  • 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
  • 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