This screenshot is of MacClade 4, not Mesquite. It is shown as a reminder that MacClade 4 is about to come out also. It has been much enhanced over version 3 particularly in the area of molecular sequence editing. Shown is protein coding sequence with codons colored according to the amino acid to which they would be translated. The last sequence is either out of alignment or non-homologous. By using the various manual alignment tools, the user can attempt to put it in alignment. Alternatively, some of the automatic sequence alignment tools can be used.
Mesquite is not intended to replace MacClade soon in the areas of MacClade's strength. Parsimony calculations and molecular sequence editing are expected to remain more sophisticated in MacClade than Mesquite for some time to come.