Parent-Descendant tracking

• Sequences can be actively linked to each other as parent/descendants. Active links are created by all cloning related operations.
• When a parent sequence is edited, Geneious can propagate the changes to all actively linked child sequences, save the changes to a copy or deactivate the links. ^Pro-only
• Documents can also be inactively linked to each other which means there is a record of their relationship but changes cannot be propagated. All non-cloning operations create inactive links.
• New lineage view shows parent and descendant relationships, including active and inactive links and the operations that where performed.

Sequence View Improvements

• Added 'By Direction' color scheme for coloring sequencing reads based on their direction
• Statistics show mean forward/reverse coverage of the selected region ^Pro-only
• Improved performance when viewing contigs with regions of very high coverage (e.g. 5,000+)
• Separated "Find in annotations" and "Find in Sequence Names" options to allow efficient annotation searching on big contigs
• Improved performance viewing big contigs with annotated reference sequences
• Can edit the color of individual annotations ^Pro-only
• Translation now displays both amino acids for ambiguous codons that translate to 2 possible amino acids
• Go to base now uses the un-gapped position for the reference sequence in assemblies

New annotation table

• Allows bulk selection, deleting and editing of annotations ^Pro-only
• Improved performance on large data sets ^Pro-only
• Remembers column state between documents ^Pro-only
• Integrated with sequence view so it shares all the same controls ^Pro-only

Variation/SNP Finder Improvements

• Added 'Minimum Strand-Bias P-value' setting for reducing false SNPs due to sequencing error ^Pro-only
• Better identification of tandem repeat amplification/reduction ^Pro-only
• Track names added to the reference sequence now include the sample name in the track name ^Pro-only
• Added "CDS Codon Number" field to indicate which codon in the CDS the SNP applies to ^Pro-only
• Added "CDS Position Within Codon" field to indicate which position within a codon (1, 2, or 3) in the CDS the SNP applies to ^Pro-only

Other New Features:

• New Align/Assemble menu replaces the separate Alignment and Assembly buttons to make it easy to choose the correct algorithm
• De Novo Assembly: Reduced memory usage, improved performance and more accurate memory usage estimates
• Improved performance importing fasta/fastq/sam/bam files
• Files that are copied from the desktop can now be pasted in to the document table or imported using Import - From Clipboard in the File menu.
• Primer Trimming: Improved performance (about 7 times faster) ^Pro-only
• Primer characteristics can now be used for reverse primers and primer pairs ^Pro-only
• Test with Saved Primers now records mismatch locations as annotations and in a new qualifier ^Pro-only
• Extract button added to Sequence Lengths Graph ^Pro-only
• Strip alignment columns can now strip columns containing a certain percentage of gaps ^Pro-only
• Enzymes view is now available when more than one sequence is selected ^Pro-only
• 2D DNA fold viwer added which is available on any nucleotide sequence under 3000bp in length ^Pro-only
• Distances view now has # Differences and # Identities matrices ^Pro-only
• Plugin Development/Public API: Improved documentation
• When generating consensus trees, they can now be saved to a separate document
• Can sort documents by their color (new color column added)
• Server Database: Improved performance