SpliceFamAlign & SpliceFamAlignMulti
What is SplicedFamAlign?
SplicedFamAlign is a tool for computing the alignment of a spliced CDS against a gene sequence while accounting for the splicing structures of the input sequences, and then the inference of transcript splicing orthology groups in a gene family based on spliced alignments.

Please cite:
Jammali, S., Aguilar, J. D., Kuitche, E., & Ouangraoua, A. (2019). SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. BMC bioinformatics, 20(3), 37-52.