Geneious

Geneious combines all the major DNA and protein sequence analysis tools into one application.

• Sequence alignment
• Contig assembly
• Primers
• Cloning
• Restriction analysis
• BLAST
• Phylogenetics
• Automatic publication updates

Bugs Fixed:

• Bam Import: Fixed tracks on reference sequence getting duplicated after editing the imported contig
• Bam Import: Names of imported documents now include the bam name as well as the reference sequence name
• Contig/Alignment View: Improved handling of annotations on circular alignments so that you can manually annotate regions of sequences that wrap past the origin and the mini-map is correct
• Contig/Alignment View: Fixed misleading #bp message next to the mouse when selecting regions to distinguish between bp and gaps
• Map to Reference: Fixed crash when selecting a sequence search result as a reference sequence
• Find Variants/SNPs: Fixed so that merged variant frequencies aren't lower than expected when some reads only partially intersect the variant region
• Gibson Assembly: enabled assembly using RNA sequences
• Import Fasta: remembers whether to import as alignment or separate sequences when importing multiple fasta files
• NCBI Search: Removed Molecule Type filter because it's not supported by NCBI any more
• Document Notes: Fixed tooltip that sometimes extended outside the monitor
• CRISPR Finder: Fixed problem when run on sequence lists of only one sequence
• Generate Consensus Sequence: Improved performance and fixed occasional out of memory error
• Wrapper Plugins: removes empty additional commands to prevent the command line tool from crashing
• Extract & Translate buttons on annotations from multiple alignment documents shows message to perform the action from the Tools menu instead
• Expression Analysis: Fixed crash when working with data sets where all reads map outside of CDS annotations
• Sequence Viewer: Tweaked so that full names don't pop out until 0.5 seconds after you stop moving the mouse
• Sequence Viewer: Fixed hang when editing lots of trim annotations
• Sequence Viewer: Fixed hang when trimming lots of annotated sequences
• Find Variants/SNPs: When run on multiple contigs, it now prompts whether or not to apply the changes to referenced documents
• Find Variants/SNPs: Fixed so that merged variants which have a range of frequencies state the frequency range instead of just the maximum frequency
• Find Variants/SNPs: Fixed so that merged variant frequencies aren't lower than expected when some reads only partially intersect the variant region
• Find Variants/SNPs: Added "Variant Raw Frequency" property
• Strip Alignment Columns: Fixed issue causing it to create inefficient alignments which would cause the alignment viewer to hang on large alignments
• Contig Viewer: Fixed hang sometimes right clicking when a large region (100,000 + sequences) is selected
• Contig Viewer: Fixed crash if you pick black as a paired distance color
• Export: Fixed crash sometimes when exporting documents with parents and descendants
• Export: Reduced size of Geneious format exported documents
• Fixed crash sometimes working with over approximately 250 million paired reads
• Biocode plugin: Fixed PCR plate primers going missing (bug introduced in 8.1.0)
• RAxML, FastTree, Garli: Fixed crash shortly after running one of these for the first time
• Dropbox: Fixed crash when you have partially synchronized your data with Dropbox and DropBox has created "conflicted copy" files in your Geneious database. Using Dropbox like this can lead to data loss so we strongly advise against using it.
• Workflows: Fixed crash when running Filter workflow on multiple documents
• Translation: Change translation of ambiguities (e.g. N) to translate as X instead of ?
• Shutdown: Fixed hang sometimes when shutting down Geneious
• Map to Reference: Tophat with Bowtie2 now accepts pre-built bt2 or bt21 index files
• De Novo Assembly: No longer produces circular assemblies sometimes from contigs containing only two sequences
• Lineage: Fixed so that lineage view includes documents selected by the new document chooser introduced in 8.1 for reference assembly, primer design and gibson cloning
• Shared Database: Greatly improved start up time when the database has a lot of folders
• Codon Optimisation: Removed incorrect message being displayed about no results being found
• Codon Optimisation: Now optimises stop codons
• Document Notes: Fixed failures when entering special characters