Geneious Pro 5.1 Beta Available Now! Print
Written by Virginia Gonzalez   
Wednesday, 18 August 2010 12:14

Making software that inspires researchers is all about listening to our customers, and many of the new features in Geneious Pro 5.1 are responses to your requests. If you have been anticipating or requested these features then download Geneious Pro 5.1 beta now to test-drive them before the full version arrives. You can also request features you'd like to see in future versions on our userforums.
Here's a taste of the customer requests we've added to inspire you to deliver better research. The number of improvements we've made is astonishing:

Multi-core capabilities with the Geneious Assembler
Assemble to multiple reference sequences at once
High/Low coverage finder to identify over or under expressed genes
Primer database browser for primer sets
Ultra-powerful batch rename with new interface
Backup all data button
Local realignment of part of an existing alignment
Automatic annotation transfer on alignments
Dot-display option in alignments
Digest by single enzymes in all relevant viewers
Interactive distance matrix viewer
Add unaligned sequence to alignment manually
GC content graph
Ligate individual sequences to re-circularize
Vector NTI gel archive importer (.ga4)
For a full list of new features see the features page

As always, if you currently own a valid license of Geneious Pro your upgrade is FREE. If your perpetual license is expired, upgrade for just 20% of the purchase price.

Register for the Geneious Server Public Beta
Geneious Server 1.0 Beta will be publicly available in a few weeks for researchers who want to evaluate how it will address high-intensity computing for NGS assembly, Phylogenetics and Sequence Analysis. The public beta trial will be available to all institutions that have a suitable testing environment. Due to anticipated high demand, there will be a registration process. To register your interest and receive information about becoming a public beta tester, contact our Market Development Manager, Dr. Peter Meintjes ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).

New Plugins to extend Geneious Pro
Interpro Scan 0.1.6 by Michael Thon is now available through the Geneious Plugin Manager
MAFFT Plugin updated to version 1.1 (compatibility fixes)
Species Delimitation Plugin updated to version 1.3 (improved efficiency)
"Out of all the software that I have tested or used in the past, Geneious is the easiest to work with in an intuitive way. The few questions that I couldn’t quickly find answers to were answered by customer support very quickly."Dr. Edward Walker - Bicycle Therapeutics

Win the World's fastest laptop
There are still two weeks remaining to get yourself into the draw to win a Dell Precision M4500 laptop plus two extra years of Geneious Pro licensing, support and upgrades. With a 250 GB hard-drive, 8 GB RAM and 64-bit addressing, there’s enough space and memory to assemble sequences easily on the move. The M4500 features:

Supreme Horsepower: Intel® Core™ i7 Extreme Edition processor, Genuine Windows® 7 Ultimate, and NVIDIA® Quadro® FX 1800M graphics
Innovative Options: Choose an optional SSD MiniCard for additional high-performance data storage
Reliability & Compatibility: Globally available and compatible with the entire Dell™ Latitude™ E-Family product portfolio

Simply purchase any individual student or academic perpetual license for Geneious Pro during August and you’ll automatically go into the draw. The winner will be announced in September. See the news page on our website for details.

How to detect SNPs and INDELs in Geneious Pro
SNPs and INDELs can be detected on two types of data files: sequence alignments and contig assemblies. In both cases, you can call all the SNPs and INDELs at once, on data with or without a reference sequence. One common workflow is looking for SNPs and INDELs between sample data and a reference sequence after performing a mapping assembly with some Next-Gen data (e.g. Illumina) to that known reference sequence. If that reference sequence has annotations, Geneious Pro can do even more of the work for you!

To begin detecting SNPs and INDELs, take the resulting contig file of your mapping assembly and click on the ANNOTATE & PREDICT menu and choose FIND VARIATIONS/SNPS. The dialogue box that opens presents a range of options that give you control over how Geneious will call each of the SNPs. You can increase the minimum coverage and the minimum variant frequency to give yourself more confidence in the call that you'd like to make. If you have a genome that's annotated with CDS regions, you can also tell Geneious Pro to look only inside CDS regions and only to call a disagreement as a SNP if it has an effect on the protein sequence (i.e. non-synonymous mutation). Click OK to annotate all the SNPs and INDELs on your assembled contig at once.

To analyze these SNPs and INDELs further, you can switch from the Sequence View to the Annotations View, click on the TYPES drop down menu, and choose SHOW ONE -->POLYMORPHISM. You'll probably have more columns displayed than you actually need, so choose only the columns you're interested in, by clicking on the COLUMNS drop down menu to get a beautiful table summary. Remember, the Annotations View is interactive, so you can FILTER, or SORT by the column headers too!