Changes in version 1.1.6: o plotAlignments can now mark codon boundaries if codon frame is specified. o Added citation Changes in version 1.1.5: o More flexible specification of strand with new readsToTarget parameter 'orientation' o Fixed warning caused by implicit embedding of S4 objects o Added tests for 'plotAlignments' and 'annotateGenePlot' o Minor speedup and internal restructuring of 'annotateGenePlot' o Added CRISPR biocView o Changed NEWS to rd format Changes in version 1.1.4: o Fixed a bug that prevented SNV settings being used in some circumstances Changes in version 1.1.2: o new function consensusSeqs returns the consensus sequences of the variant alleles