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Over 35 new features available now in Geneious Pro 5.0 PDF Print E-mail
Written by Virginia Gonzalez   
Wednesday, 26 May 2010 11:57

The new improved Geneious Pro 5.0 is out and available to download now. This major new version of Geneious Pro includes numerous features suggested by our users and is packed full of new features to inspire you to deliver better research.

"Geneious is really the perfect software package for bioinformaticians, molecular biologists, and even clinical researchers, combining both power and ease of use. I am particularly impressed by the capability of the software to assemble millions of paired-end reads de novo from metagenomic data."Dr Charles Chiu - Assistant Professor, University of California San Francisco School of Medicine

Want to see the new features of Geneious Pro 5.0 in action without downloading it? Sit back, relax and enjoy our 3-minute video: http://www.geneious.com/whats_new_video

Paired-end reference assembly
Paired-end de novo assembly
Paired-end sequence visualization
5x to 10x more efficient memory use and loading speed for large contigs SNP/Variation finder
Deleted items (recycle bin/trash) to restore previously deleted items
Split view to visualize your sequence in multiple different viewers
RNA and primer secondary structure (RNA fold in the Vienna package)
Microsatellite data (.fsa) viewer (take our survey about this feature)
.caf, .fsa, .maq and .sam file format importer
.eps, .fastQ and .qual exporter
Document history
For more details visit the new features page of our website

How to call secondary peaks in Geneious Pro
Calling the secondary peaks of chromatogram data is easy in Geneious Pro, but first requires that you install the heterozygotes plugin. In the preferences, go to plugins and features and select the heterozygotes plugin from the available plugins. From the sequence menu, select find heterozygotes and choose a peak similarity percentage that matches the type of biological question you're trying to answer (~50% for heterozygotes, or lower for identifying rare alleles or variants). Choose either to annotate the secondary peaks on the sequence, or to alter the sequence itself to contain the ambiguities introduced by the secondary peak call. For further assistance, email This e-mail address is being protected from spambots. You need JavaScript enabled to view it .

"Geneious has several capabilities that have really simplified and sped up my data analysis and interpretation! I can now move fluidly from primer design, to sequence assembly, to analysis within one platform. Further, the new Sequencher contig import option in 5.0 beta allowed me to recover years of prior analyses with little problem."Dr Sher Hendrickson - Laboratory of Genetic Diversity, National Cancer Institute

Coming soon: Geneious Server™
The Geneious Server private beta will kick off in June with a select group of institutes putting it through its paces. For those of you eager to try out Geneious Server, there will be a public beta trial of Geneious Server in six to eight weeks’ time. This will allow you to test a more stable version of the beta software and provide your feedback at any time to our development team.

Geneious user plugins
Our customers continue to develop useful plugins for Geneious Pro - below is a new one we'd like to share with you.

If you have a plugin that you'd like to share with our development team or with other Geneious Pro users, head on over to our userforums and let us know. Our development team can help you with troubleshooting, make suggestions for improvements and we'll feature your plugin right here when it's ready to be tried out en masse.

InterProScan beta plugin by Michael Thon
Michael Thon from the University of Salamanca, Spain has developed a plugin that submits protein sequences to the InterProScan server at EBI, and then parses the results, creating annotations on the proteins without having to leave the Geneious Pro interface. The annotations that are returned include protein domains from any of the 12 InterPro member databases as well as the InterPro terms themselves.

Geneious Travel Plans for 2010
The Biomatters' team will be attending the American Society for Microbiology (ASM) conference in San Diego, the Evolution2010 conference in Portland, Oregon and the Intelligent Systems for Molecular Biology (ISMB) conference in Boston. If you'd like to catch up with us, either visit our booth on the day or email This e-mail address is being protected from spambots. You need JavaScript enabled to view it and arrange a time for a chat.

Summer in the Northern Hemisphere also marks the beginning of customer visits in the USA to talk about Geneious Pro 5.0 and Geneious Server. Visits typically involve giving a presentation on the major features and up-coming functionality of Geneious Pro, taking feature requests, learning more about how we can make Geneious Pro even better for your research and discussing site-license solutions with management. We've published our travel itinerary, so if you would like us to visit your university or institution in the future, please get in touch via the links on the new travel plans page on our website or by emailing This e-mail address is being protected from spambots. You need JavaScript enabled to view it .