Complete-Deletion Option

In the complete-deletion option, sites containing missing data or alignment gaps Phylogenetic analysis on two or more DNA or amino acid sequences requires that the sequences be aligned so that the substitutions can be accurately enumerated. During alignment, gaps must be introduced in sequences that have undergone deletions or insertions. These gaps are known as alignment gaps or indels. are removed before the analysis begins.  This is in contrast to the pairwise-deletion option In the pairwise-deletion option, sites containing missing data or alignment gaps are removed from the analysis as the need arises (e.g., pairwise distance computation). This is in contrast to the complete-deletion option in which all such sites are removed prior to the analysis. in which sites are removed during the analysis as the need arises (e.g., pairwise distance computation).