The Welcome “project” opens when you launch MegAlign Pro, and is used for creating or opening projects. As you add projects, the Welcome “project” will remain as the leftmost tab unless you manually move or close it. Note that 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 open an existing MegAlign Pro project (.msa):

Do any of the following:

  • From the Welcome tab, click Open Project on the left. Then use the options on the right to Open alignment project or open a recent document.

  • Drag an .msa file from the file explorer or desktop and drop it on an empty MegAlign Pro project window or tab.
  • Choose File > Open from the menu.
  • Click the Open a file tool ().
  • Press Ctrl/Cmd+O.


To create a new MegAlign Pro project:

Do any of the following:

  • From the Welcome tab, click New Project on the left. Then choose one of the options on the right:



    • New blank alignment project – Opens an empty project window.

    • New alignment – Launches a file chooser. Choose files and press Open to create a new MegAlign Pro project with the default alignment already in progress.

    • New alignment with options – Launches a file choose. Choose files and press Open to create a new MegAlign Pro project with the Align Sequences dialog open. Specify the alignment algorithm, change other settings as desired, then press Align to begin the alignment.
  • Choose File > New Alignment Project from the menu. 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 and add sequences to it simultaneously, drag sequence files from a file explorer and drop them on the project tab row of the MegAlign Pro window.
  • Click the Create a new alignment project tool ().
  • Press Ctrl/Cmd+N.


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

  1. Do either of the following:

    • From the Welcome tab, click Open Project on the left. Then use the option Import alignment on the right.

    • 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.


To open a Newick-format tree file:

See Phylogenetic Trees.

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