We propose PhyloSofS, the first automated tool to reconstruct plausible evolutionary scenarios explaining a set of observed transcripts, and to generate 3D molecular models of the protein isoforms. We apply it to the JNK family (60 transcripts, 7 trees) to identify AS events of ancient origin and relate their functional outcome with changes in the protein dynamics. We also show that PhyloSofS can help identify new potential therapeutic targets.
