One large project I am working on involves sequencing the genomes of many hundred Eucalyptus individuals across the section Adnataria (subgenus Symphyomyrtus). The Eucalyptus reference genome is of E. grandis, in an adjacent section within the same sub-genus. Molecularly, this equates to something in the order of 5% of sites diverged between most Adnataria and the reference. Therefore, care is needed when aligning short reads to the reference. The aligner should be sensitive enough to align short reads to a reasonably diverged reference, without increasing the number of false-positive or otherwise erroneous alignments.