To export alignment to a new document in a required format select a single object with an alignment in the Project View window and click the Export/Import ‣ Export object context menu item:

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The Export Document dialog will appear:

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Here it is possible to specify the result file location, to select a sequence file format, to define whether to keep or remove gaps (‘—’ chars) in the aligned sequences and optionally add the created document to the current project.

Here you may select the name of the output file in the Save to file field and, optionally, choose the format of the output file in the File format field. Use the Compress file checkbox to compress the file. The Add to project checkbox, checked by default, adds the output file to the current project. After choosing all parameters click the Export button.