MEGA provides a utility for concatenating multiple files containing sequence data into a single sequence alignment. This tool is used as follows:
All of the source alignment files that are to be concatenated should be collected and placed together into a directory/folder on your computer. There should be no other files in this directory and all of these files should be FASTA formatted files or MEGA formatted files. The data must all be of the same type as well (cannot mix DNA and amino acid data).
From the MEGA main form, click Data->Concatenate Sequence Alignments. MEGA will prompt you for the directory/folder that contains the source alignment files and you should select that directory.
If MEGA cannot infer the data type contained in the files, MEGA will prompt you for the data type (as well as special symbols used such as for indels or identical bases).
MEGA will process the input files in alphabetical order, concatenating sequences that have the same name and adding a new sequence when a new name is encountered. Wherever needed, MEGA will add missing base symbols (default is ?) to fill missing data so that sequence data alignment is maintained. For example, if a new sequence is encountered in the third file processed, missing base symbols (equal to the number of bases from the first two files) will be pre-pended to the new sequence.
Once the concatenation is complete, the data will be imported into the Sequence Data Explorer window (press f4 or click View->Explore Active Data on the main form to view the alignment).
From the Sequence Data Explorer, you can export the concatenated alignment to multiple formats by clicking Data->Export Data...