In the partial-deletion option, sites are removed before the analysis begins. A site is removed if it has a higher percentage of ambiguous sites than is specified in the Site Coverage Cutoff parameter. This is similar to complete deletion, in that it will have the same result if the Site Coverage is set to 100% (because 100% means there are no ambiguous sites). This along with complete deletion is in contrast with the Pairwise-deletion in which sites are removed during the analysis as the need arises (eg., pairwise distance computation).