The Welcome “project” opens when you launch MegAlign Pro and is a central location for opening projects, searching NCBI databases, getting help, and much more. As you add projects, the Welcome “project” will remain as the leftmost tab unless you manually move or close it. We recommend leaving the Welcome tab in place, since it has many time-saving shortcuts to useful commands.
| Tab on left | Option on right | Shortcut to this procedure: |
|---|---|---|
| New project | New blank alignment project | File > New Alignment Project > Blank Document. (see Create or Open a Project). |
| New alignment | File > New Alignment Project > Blank Document plus File > Add Sequences plus Align using default method and options. (see Create or Open a Project). | |
| New alignment with options | File > New Alignment Project > Blank Document plus File > Add Sequences plus Align with Options (allows you to choose the method and edit options). (see Create or Open a Project). | |
| Align viral genomes using reference | File > New Alignment Project > Blank Document plus File > Add Sequences plus Align with Options set specifically to use the MAFFT alignment algorithm. (see Create or Open a Project). | |
| Filter and align sequences | File > Add Sequences with Filter (see Add only sequences that meet filtering thresholds). | |
| Align by gene homology | Align > Align by Gene Homology (see Perform a gene homology alignment). | |
| Open project | Open alignment project | File > Open (see Create or Open a Project). |
| Import alignment | File > Import Alignment (see Create or Open a Project). | |
| Recent documents | File > Recent Documents. (see Create or Open a Project). | |
| Search | Search for sequences | Search > Search for Sequences (see Search for sequence matches in BLAST). |
| Search for text in NCBI nucleotide | Search > Search for text in NCBI nucleotide (see Search for text or accession number matches in Entrez). | |
| Search for text in NCBI protein | Search > Search for text in NCBI protein (see Search for text or accession number matches in Entrez). | |
| Training | User guide | Help > User Guide. Opens this User Guide. |
| Tutorials | Opens this User Guide to the MegAlign Pro Tutorials topic. |
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