Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment sequences. By entering a group of sequences into MegAlign Pro using a special command, the entire data set will be concatenated end-to-end and treated as a single multi-segment sequence.

Suppose you want to string together the consensus sequences from all the contigs in an assembly, or chromosomes in a genome, or exons in a gene, etc. If you enter these sequences using File > Add Sequences or the corresponding button (), you will end up aligning the parts to one another. To avoid this, use the following procedure:

To add sequences end-to-end:

Choose File > Add Sequences End-to-end, select the Add sequences end-to-end in project tool (), or press Ctrl/Cmd+Shift+E. The following dialog appears:

  • To name the group, type a name in the Group name box. This serves as a substitute for a regular sequence name in all the MegAlign Pro views. If you do not explicitly type a name into the Group name box, a default name will be computed from the items in the list.
  • To add a sequence file to the left-hand pane, click Add. Alternatively, you may simply drag files from any file explorer & drop them into the main part of the dialog. Any supported MegAlign Pro file type may be added.
  • Each group of multi-segment sequence should have its segments arranged in the same order relative to other groups. To reorganize sequences, select a sequence in the left pane and then use the Up or Down buttons to move it to the desired position.
  • To remove a sequence from the left-hand pane, select it and click Remove.
  • To add another group of sequences after you save the current group, leave the Add another box checked. Otherwise, remove the check mark.

Click OK to keep your changes and add the sequence group(s) to the project, or Cancel to leave the dialog without adding the sequence group(s) to the project.

Unless you unchecked the Add another box, a new Add Sequences End-to-end dialog will appear after you check OK. If you don’t have any additional groups to add, you can exit by pressing Cancel.

To edit an existing end-to-end group:

Select an aligned or unaligned sequence group in any view and choose Edit > Edit Sequences End-to-end.

If you select an aligned sequence and then apply changes in this dialog, the sequence will be removed from the alignment and placed in the “Unaligned Sequences” area. Because of this possibility, you must respond OK to the following prompt before the dialog will open:

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