After using File > Rename or File > Rename with Fields, the custom names are only exported as part of the sequence data in certain cases. Raw data sequences imported into MegAlign are never modified in any way, and always retain their original names.

The following table lists the cases in which custom sequence names are exported:

Export target Notes
MegAlign Send an alignment to MegAlign using File > Send to MegAlign. Or use File > Export Data, save as a MegAlign (.meg) file and then open the file in MegAlign. In either case, MegAlign truncates imported labels to a maximum of 39 characters.
Tree viewers Send an alignment directly to a tree viewer with File > Send Tree to (Tree Viewer). Or save a tree file via File > Export Data > Tree, and then open it in a tree viewer. The custom label will be retained.
Sequences and alignments Custom labels are exported to Nexus, and MegAlign formats. They are not exported to FASTA or GenBank formats.
Distance matrices Custom labels are exported to distance matrices of all formats (e.g., .csv, .tab, .dst, and .nex).

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