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.

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

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