Multiple Sequence Alignment
Try and re-assign the sub-exons that do not align against any other sequence in the MSA to another cluster (disabled by default).
Turn off the refinement of s-exons through shifting of the very small sequence stretches isolated by gaps (enabled by default).
Turn off the refinement of s-exons through disintegration of the 1-column s-exons (enabled by default).
Alternative splicing event detection
List of transcript features (column names in the path_table) separated by commas or line returns used to sort the transcripts (rows in the path_table).
Turn off the removal of s-exons that appear in only one transcript (enabled by default).