There are a variety of ways to create a new MegAlign Pro project, whether a blank project, one that is prepopulated with sequences, or even one that is prepopulated and with the alignment already in progress.
| Task | How to |
|---|---|
| Create a new blank project | Do any of the following:
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| Create a new project, add sequences to it, and align using the default method | From the Welcome tab, click New Project on the left, and then choose New alignment. This launches a file chooser. Choose files and press Open to create a new project with the default alignment already in progress. |
| Create a new project, add sequences to it, and choose the alignment method when prompted | From the Welcome tab, click New Project on the left, and then choose New alignment with options. This launches a file chooser. Choose files and press Open. Alternatively, you can drag sequence files from a file explorer and drop them on the New alignment with options icon. In both cases, a new project is created that contains the sequences. The Align Sequences dialog open automatically so you can specify the alignment algorithm and change other settings as desired. Press Align to begin the alignment. |
| Create a new project for aligning viral genomes to a reference | From the Welcome tab, click New Project on the left, and then choose Align viral genomes using reference. This 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. |
| Create a new project that contains a filtered subset of sequences | From the Welcome tab, click New Project on the left, and then choose Filter and align sequences. This 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. See Add only sequences that meet filtering thresholds for instructions. Only the sequences that meet the specified criteria will be added to the project. |
| Create a new project for finding homologous genes | From the Welcome tab, click New Project on the left, and then choose Align by gene homology. This opens the Gene Homology setup wizard, starting with the Reference Sequence screen. |
| Create a new project containing the currently selected sequences | Use the menu command File > New Alignment Project > With Selected Sequences. If no sequences are selected, this option is disabled. |
| Create a new project containing the currently selected subsequences | Use the menu command File > New Alignment Project > With Selected Subsequences. If no subsequences are selected, this option is disabled. To learn how to select a range of the sequence in one or more sequence rows (e.g., the sequence corresponding to a feature), see Make a Selection. |
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