To open an existing MegAlign Pro project (.msa):

Use the File > Open command, select the Open a file tool (), or press Ctrl/Cmd+O. Once a project is open in MegAlign Pro, you can open additional files using the same command.

If you moved or renamed any of the sequences prior to reopening a project, you may be prompted to supply the new name(s) or navigate to the location(s) of those sequences.


To create a new, untitled MegAlign Pro project:

Choose File > New Alignment Project, select the Create a new alignment project tool (), or press Ctrl/Cmd+N.

Three options are available:

  • Blank Document – Creates an empty document, regardless of whether any sequences or subsequences are currently selected. See Add ungapped sequences to a project for an alternative method.
  • With Selected Sequences – Creates a new document containing the currently selected sequences. If no sequences are selected, this option is disabled.
  • With Selected Subsequences – Creates a new document containing the currently selected subsequences. If no subsequences are selected, this option is disabled.


To create a new project while simultaneously adding sequences to it:

Drag and drop sequence files into an empty project or onto the tab row above one or more projects.


To create a new project based on a classic MegAlign project file or a gapped FASTA file:

  1. Choose File > Import Alignment.
  1. Navigate to the file you wish to open. The file must be in MegAlign (.meg) or gapped FASTA format (.fasta, .fas, .fap, etc.).
  1. Click Open.

The project will open as a MegAlign Pro project in a new tab.

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