where to start (Score 1)

There are many Linux tools. But you want to start by understanding the problem space. "Bioinformatics for Dummies" is a great place to start; although it is web-oriented, many of the programs are downloadable for linux. But really, try to get a deeper understanding of the problem - Mount's text "Bioinformatics" is well worth the money, and the second edition looks like an improvement in many ways - and the reference everyone uses (but this will induce pain) is "Biological Sequence Analysis". These three books and being in a lab will make things move very fast. Ok, if you must get a fast answer... download EMBOSS for the set of well-tested robust utilities (warning: installation a slight pain) and NCBI's blast for sequence alignment. Then write scripts to integrate. Fast easy robust.