The Homology filter tries to filter out gene pairs by comparing the homology of the two corresponding exons. The idea behind this filter is similar to the Alternative Alignment filter (AAF), however this approach is more computationally intensive and less potent than the AAF and should be used only when the AAF is not applicable (e.g. the SAM XA Tag is not available and a new alignment is not feasible). Homology Indel Malus and Homology Mismatch Malus define the malus added to the alignment score in presence of an indel or a mismatch, respectively. The Match Gain indicates the bonus added to the alignment for each match. The Homology Continuity Gain is a further bonus added to the score in presence of a stretch of continuous matches. The Homology filter is inactive by default.