Homolmapper scoring algorithms. [A] Scoring of gaps and insertions. A sample alignment is shown (1), with the calculated homolmapper scores for each position shown for the available gap and insertion scoring algorithms (2), with non-zero scores highlighted by color. Gaps and insertions are always scored relative to the sequence matched to the structure (MATCHED_SEQ for this example) The positions in the alignment that give rise to those scores are shown in the same color scheme. Gap length is the length of the gap in the matched sequence relative to others (green), while gap frequency is determined by the number of sequences having any residues in the gap (blue). Insertion length is not calculated across gaps (purple). Insertion frequency is determined by sequences having residues at each position (red). [B] Scoring with user-defined amino acid sets, using the alignment from [A]. For the "degen" case, Asp and Glu are considered equivalent, and the percentage of sequences with Asp or Glu is reported for each position. For the "sloppy" example, Asp and Glu are considered equivalent members of a single set, Arg and Lys are considered equivalent members of a second set, and all other amino acids are considered to be unique members of their own sets. In this example, the alignment is scored relative to the matched sequence. The sets assigned to each amino acid in the structure are also shown.