Dear developers of branchpointer,
following the recommendations of a recent review paper on branchpoint prediction tools, we are using branchpointer in the context of alternative splicing. Generally, this works very well, and the results look reasonable. However, we want to follow up on specific effects that seem to affect 3' splice sites with very close branch points, 10-20 bases upstream the AG. Is it possible to tweak branchpointer to score these close branchpoints?