Trinity

Trinity can be found in /opt/trinity-2013.02.25/  
This version of trinity uses Bowtie 1 which can be found here /opt/bowtie1-1.0.0/   There is also Bowtie 2 installed on the cluster here /opt/bowtie2-2.1.0/   If you use trinity you will need to add /opt/bowtie1-1.0.0/bin/ to your PATH variable.