Pairwise-deletion option

In 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., 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 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.