Alternative splicing detection using RNA-seq

[jiwu2573]

I used Bowtie and Tophat to align my reads and to identify splice junctions but now i would like to be able to compare my two conditions.

I am looking for something that uses mRNA-seq to identify novel splicing events in a given sample or, if multiple samples are available, identifies differential splicing events between those samples.

Has anyone come across some software that can do these things?

Thanks in advance.