In MEGA, gap sites are ignored in the MP analysis, but there are three different ways to treat these sites. One is to delete all of these sites from data analysis. This option, called the Complete-Deletion option, is generally desirable because different regions of DNA or amino acid sequences often evolve under different evolutionary forces. However, if the number of nucleotides (or amino acids) involved in a gap is small and gaps are distributed more or less randomly, you may include all such sites and treat them as missing data. Therefore, gaps and missing data are never used in computing tree lengths. The final option is Partial Deletion which deletes the gaps assuming there are less than a certain percentage of gaps (unambiguous).