Geneious - 4.8

• Fast de novo assembly - Capable of assembling 100,000 454 reads or 500,000 Illumina Solexa reads without a reference sequence in a few minutes on a desktop machine.
• New dotplot - capable of dotplotting genome sized sequences with brand-new controls (utilizes EMBOSS)
• Better handling of next-gen sized data - greatly improved speed and memory efficiency when dealing with large next-gen data sets
• Primer extension support - add a restriction site or other extension to primers and Geneious takes this in to account when testing the primer and using it for other analysis
• Trim by primers - screen for primers from the local database
• Batch export - export several documents to separate files in one step (File > Export > Batch Export)
• Color sequences according to their annotations ("By Annotation" option under Colors in the Sequence View)
• More powerful primer design on alignments and support for designing primers on assemblies
• FastQ file format import
• CsFasta file format import
• Qual file format import
• Add and Remove enzymes from enzyme sets and combine enzyme sets
• Search for individual primers from your database that match a sequence
• Option to find residues in the translation of DNA (Edit > Find in Document)
• Quality measures for chromatograms added to sequence view statistics (Confidence and Expected Errors)
• Extinction coefficient for proteins added to sequence view statistics
• Read length and coverage statistics for sequencing data added to sequence view statistics
• Sort sequences by name and other attributes in sequence lists, alignments and assemblies (right click in Sequence View and under Properties options)
• The EMBOSS tools plugin is now included with Geneious as standard (adds many functions)
• All models in a 3D structure can now be shown simultaneously in the 3D structure view
• Folders can now be copied between server and local database by drag and drop

New features:

• Pan in Sequence View by holding Ctrl+Alt while dragging (Command+Alt on Mac OS)
• Greatly improved local database start up time for users with large numbers of documents (takes effect after first start up of 4.8)
• Geneious export no longer offers compressed/uncompressed format, Geneious format is always compressed with .geneious extension
• Sequence view statistics can now be copied to the clipboard
• Improved display of multi-interval annotations and primers in the sequence view

Bugs fixed:

• Change residue numbering now works on circular sequences
• Notes can now be stored in the Server database