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 chooser. 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.

    • Align viral genomes using reference – Launches a file chooser. Choose files and press Open to create a new MegAlign Pro project and open the Align Sequences dialog for the MAFFT multiple alignment algorithm. Use the Reference Sequence drop-down menu to specify the sequence to use as the reference and change any other desired settings. Press Align to begin the alignment.

    • Filter and align sequences – Creates an initially blank project, prompts you to select sequences from a file chooser, and then opens the Filter Sequences dialog. Set up any desired filters and press the Filter button. Only the sequences that meet the specified criteria will be added to the project.
  • 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.

If you elected to open a blank project, see Sequences to learn how to add sequences to it.

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