Comparison of UCSC liftOver with OrthoINDEL. Briefly, CrossMap splits syntenic regions into fragments separated by any gap in the alignment. OrthoINDEL concatenates the fragments split by indels and returns syntenic regions containing these insertions and deletions (indels). UCSC liftOver does not convert the third example (yellow), in which a large portion from the species1 region is absent in species2. OrthoINDEL enables us to retrieve syntenic regions with large indels and filter out other SVs such as inversions. Rectangles represent one-to-one alignments from species1 to species2. Diamonds represents insertions in species1. Triangles represents an inverted region between the two species.
