R9.0 was released on October 06, 2015.

Geneious R9.0

Golden Gate

Intelligent handling of preconfigured Golden Gate parts and automatic designing of primers for new parts.

RNA- Seq and Structural Variant Mapping

Map RNA-seq using existing annotated coding regions or discover novel intron and fusion genes during mapping. For DNA sequencing, you can now discover structural variants and annotate them, allowing for correct alignments of read-ends around deletions and structural rearrangements in heterozygous samples.

Big Trees

New search box for finding nodes and taxa, and automatic collapsing of sub-trees based on distances. Greatly improved performance when loading and rendering trees.

Cutting edge CRISPR

New scoring strategy for on-target activity. Options to control how many mismatches and indels are allowed when scoring against off-targets.

VCF Export

Easy exporting of single-sample variants.


Brand new and super-fast de novo assembler with a very low miss-assembly rate.

Primer Design

Improved the speed on larger sequences when a target region and product size range have been specified

Read filtering with built-in BBTools

  • Merge paired reads using BBMerge
  • Error correction and coverage level normalization using BBNorm
  • Duplicate read removal using BBDedupe
  • BBDuk plugin for additional trimming (provides adapter, paired read overlap, quality, minimum length, and entropy trimming)

New Plugins

  • BBMap mapper for DNA/RNAseq
  • EupathDB for searching and retrieving eukaryotic pathogen sequences
  • Repeat Finder for annotating all regions that are repeated elsewhere in a sequence

Release Notes

View detailed Geneious R9.0 Release Notes

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