Data | Export Data
The Exporting Sequence Data dialog box first displays an edit box for entering a title for the sequence data being exported. The default name is the original name of the data set, if there was one. Below the title is a space for entering a brief description of the data set being exported.
Next is the option for determining the format of the data set being exported; MEGA currently allows the user to export the data in MEGA, PAUP 3.0 and PAUP 4.0 (Nexus, Interleaved in both cases), and PHYLIP 3.0 (Interleaved). tA the end of each line, is "Writing site numbers." The three options available are to not write any number, to write one for each site, or to write the site number of the last site.
Other options in this dialog box include the number of sites per line, which codon position(s) is to be used and whether non-coding regions should be included, and whether the output is to be interleaved. For missing or ambiguous data and alignment gaps, there are four options: include all such data, exclude all such data, exclude or include sites with missing or ambiguous data only, and exclude sites with alignment gaps only.