Zientzilaria

Covering the bioinformatics niche and much more

First Post: A Take on Geneious

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Geneious is an excellent bioinformatics software created by Biomatters, a wonderful company from New Zealand. When they released the first version of the software I was delighted to write a review of it. So here is my first take on Geneious from 2006. I will be back with more comments on the program on the other side of this post.

Geneious review

After installing Geneious and running it from the command line (double clicking if you are a Windows user) you don’t see anything special about the software. Apart from the nice looking interface there are no fancy buttons, no pop-up messages, no hints (maybe just the tutorial tab on the right side) and no clutter.

After the first minute staring at its interface you wouldn’t say that this is one of the most innovative software to appear for molecular biology, phylogenetics, bioinformatics and other fields of science. You wouldn’t say, but after playing for an extra five minutes the only sound in your mind would be “Wow!!”. Geneious is wonderful work of a group of bioinformaticians that decided to make science easier to do, at least when doing computer work.

Geneious is really genial. Basically you don’t have to do anything, the program does for you. OK, maybe you have to do something but the program seems to know what you want to do. Import a sequence into it: Geneious knows if it is nucleotides or amino acids. Do you have an annotation for your sequence? Nice, Geneious will display it for you. Structure of your protein? There it is, just select the tab. You don’t have to save anything: it is already there automatically saved for you, just like your personal GenBank, PDB, Swissprot.

And the software can do more, much more. Have internet? (Who doesn’t?) There is a direct connection to NCBI and no worries about formatting searches, remembering parameters, Geneious does it all for you. PubMed? Check, same thing: filter your references, search by first author, date of publication, anything. If you are Linux geek, your BibTex entry is there, if you are Windows person just export it to EndNote.

Another nice addition to the program is the possibility to create agents. These agents are like your free personal search expert who is there 24/7/365. Set up an agent to a specific search pattern and it will get for you when it appears, keeping your records up-to-date even before you have breakfast.

Nothing bad can be said about Geneious, and with endless possibilities of improvement (with a looming API release soon) this is the Holy Grail of molecular biology, phylogenetics and bioinformatics software. Kudos to Geneious