Geneious: All versions - Software Informer

v8.1 [Mar 5, 2015]
Patch 8.1.6 (16 June 2015)
Bugs Fixed:
Modified Date: When editing documents, fixed bug where modified date would revert to the created date on some documents
Map to reference: Fixed iterative mapping causing reads to be mapped offset from where they should be in rare situations
Find Variants: For deletions over about 100bp, fixed incorrect average quality and p-values
Find Variants: Fixed bug where variants were not getting merged into longer variants sometimes
Find Variants: Fixed crash in some situations when working with RNA variants
Find Variants: Fixed crash when reference sequence has trimmed regions
Contig View: Hide columns over x% gaps would sometimes hide the wrong column in the right-most 8bp of the contig (the fix only applies to newly generated contigs)
Alignment View: Fixed 'Pairwise % Positive' value to ignore columns which are entirely gaps
BAM/SAM Export: Fixed so that template length (TLEN) in BAM/SAM files for right most paired read is negative
Blast2GO: Fixed crash when you have installed the Blast2GO plugin, created some results using Geneious, and then uninstalled the plugin
Shared Database / Custom BLAST: Fixed error message about data going missing when trying to view some custom BLAST results in a shared database
Shared Database: Stopped a crash that occurred when documents could not be cleared from the clipboard.
NCBI Gene DB: discontinued entries can be downloaded and won't be ignored anymore
NCBI Gene DB: Fixed failing downloads of entries with missing GenomicInfo
CRISPR Site finder: Added help button for inputting the CRISPR motif
UniVec: Updated the bundled UniVec database to the latest version
Gibson Assembly: Shows message that operation can't be performed when sequences are too short
Gibson Assembly: Fixed bug where it couldn't find some of the provided sequences in a sequence list
GenBank File Import: Fixed cases where fields were not imported if KEYWORDS didn't end with a period
GenBank File Export: Added option to export sequences with a LOCUS name longer than 16 characters

v8.0 [Oct 10, 2014]
Bugs Fixed:
- Document Table: Fixed crash sorting by URL column.
- Fix long delay starting up when using floating license on some systems.
- Find Variations/SNPs: Fixed crash in rare situations.
- VNTI Import: Fixed failure to import files containing one-line misc feature annotation.
- Sequence Viewer: Fixed crash when viewing empty or 1bp sequences with CDS annotations.
- Translation: Reverted change introduced in 8.0.1 so that CDS translations after truncated intervals were translated as ??? since we can't be sure it is in the correct frame.
- Translation: Improved extraction of CDS annotations with frame slippage so that intersecting CDS annotations without slippage are not annotated as truncated. The effect of this is that the overlapping annotation can be correctly translated too.
- Fixed an issue where some restriction site annotations from older versions of Geneious wouldn't get recognised by Digest and would crash.
- VCF Import: Fix extra annotations added when importing large size files with more than 200 unique sequences.
- Geneious Export: Fixed incorrectly formatted file when exporting sequence lists containing tracks such that importing that file into Geneious R7 or earlier would crash the old version of Geneious.
- Custom BLAST: fixed a bug where databases of stand-alone sequences types wouldn't correctly have field values that had been previously overwritten, and have the old values instead.
- Alignment Concatenation: Fixed incorrectly concatenated chromatogram when the sequence is not present in all alignments.
- SAM/BAM Export: Fixed incorrect export of qualities exceeding 93 (the maximum supported by SAM/BAM format). It now clips higher qualities to 93.
- GFF importer: fixed a bug with the where features with long parent names would be incorrectly merged into a single annotation.
- gff importer: correctly allow ? values when specifying feature strand.

v7.1 [Mar 19, 2014]
New Core Features
Molecular Cloning
Gibson Assembly - One-step cloning of fragments using Gibson assembly including automated primer design and batch cloning/shuffling
Codon Optimization - Find rare codons or produce a fully optimized sequence based on a target organism and remove unwanted restriction sites at the same time.
TOPO Cloning - One-step cloning of fragments into a vector using TOPO
Searchable, selectable and sortable enzyme table. Now has a search box to find enzymes by name
Primer Design
Dynamic Primer Design
Primers are now designed on the consensus of alignments and contigs
Redesigned Add 5' extension operation that allows adding several extension parts in one step
New in the R7 Update
Primers can now be ordered from Eurofins MWG Operon via link on the Text View of oligo sequences.
Alignment, Assembly and Mapping
Added visualization of minimum/mean/maximum coverage when zoomed out.
Added highlight coverage above threshold option.
Consensus: When coverage or quality is below a specified threshold you can choose to call either ?, N, Gap, or the reference sequence value.
New in the R7 Update
All newly created contigs will have a mean coverage field in the document table.
All newly created reference sequence contigs will have a '% of reference sequence covered' field
De novo assembly: Added option to produce circular contigs when the ends match
De novo assembly: Better results on data with gappy error models (e.g. IonTorrent or 454 data)
De novo assembly: Reduced size and improved performance on large lists of consensus sequences produced
Strip Alignment Columns: Add an option to remove columns that contain at least one ambiguity
Strip Alignment Columns: Add an option to strip two columns per codon
Annotation, Analysis and Prediction
Copy and Paste Annotations - Annotations are now maintained when copying sequences! Highlight part of a sequence, copy with ctrl c and then paste it using ctrl v into another location and the annotations will be preserved.
Exporting Graphs
New in the R7 upgrade
Compare Annotations: Easier to use interface, better results, more powerful options (including 3 way comparison), and results include annotation properties
Extract Annotations: Added options to include upstream, downstream and intergenic regions of matching annotations
Statistics: Added molecular weight of short nucleotide sequences
New Plugins
Tree Building and Viewing
RAxML - Randomized Axelerated Maximum Likelihood
GARLI - Genetic Algorithm for Rapid Likelihood Inference
FastTree - Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
Alignment, Assembly and Mapping
LastZ - BLAST-like alignment tool for the pairwise alignment of chromosome-sized nucleotide sequences
Bowtie2 - Short read aligner
Assembly
Velvet - De-novo assembler for very short reads
New in the R7 Update
TopHat- Fast splice junction mapper for RNA-Seq reads.
MIRA-Specialised assembler for sequences with a high number of repeats

v6.1 [Mar 7, 2013]
-Thermodynamic calculations
- Annotations from dbSNP now hyperlinked.
- Homopolymer quality reduction setting in Variant Caller.
- Automatic plasmid annotation
- Fine-tuning algorithm quickly generates accurate results using less memory
- Improved support for read mapping when choosing to map to multiple locations
- Number an alignment without also also numbering the reference sequence. Edit properties in sequence lists and alignments.