question: Which are currently available software tools for detecting rare codon clusters in coding sequences?
answer: Rare codon clusters (RCCs) correspond to regions along mRNA sequences where among the possible choices of synonymous codons those  with lower usage are observed. Due to the fact that relative codon frequencies have been shown to correlate with their cognate tRNA frequencies, RCCs indicate possible translational attenuation sites. A few tools specific for this task have been described in the literature, namely: LaTcOm, %MinMax, PAUSE, Sherlocc, Sliding Window (RiboTempo)