Geneious

My apologies if this is only interesting to a narrow audience, but I would like to share my experiences of some software I’ve become a fan of. First off, Geneious.

Geneious is designed as an all-in-one bioinformatics application “that is both ultra-powerful and easy to use” (Geneious website). I first came across the free version years ago, but without any need for it at that stage, I didn’t pay too much attention. During my Master’s course at the NHM, I very suddenly became aware of the computing requirement for biosystematics.

Much of the work of our lab (pretty much all of it, to be honest) is in the comparative analyses of DNA sequences from bunches of related organisms, looking for hints of shared evolutionary history to make evolutionary trees and to estimate population genetics parameters and look for signatures of particular evolutionary processes. On a day-to-day level, what this means is lots of PCR in the lab followed by sequencing, the editing of sequences, the compilation of sequences into related lists (alignments) and the computational analysis of these alignments. The way things used to be set up meant that each step in this process used a different piece of software. Predictably, this was a bit of a nightmare. We would use one application to examine the raw sequence and edit obvious errors, followed by exporting it, then importing into a different program to do the alignment, then a third program to view and check the alignment (when you might have to go back to the first one to double-check) followed by analysis in a fourth or even fifth program! Each step has its own quirks (some software likes to disagree on standardized file formats, for example) and some bits only run on macs or pcs, or only have a limited number of licenses…. Nightmare.

This was when I tried the 14 day demo of Geneious Pro. I was sold. Now it was one application for everything. It would run on macs and pcs. It could search Genbank and download sequences for you. If you change one file, it can automatically update others documents that use that file. It can handle pretty sizable datasets (big chunks of genome).

It is quickly clear that it has been designed to be as user-friendly as possible. Every change you make is flagged, making it possible to see the editing history of a file and undo catastrophic mistakes. I wouldn’t go so far as to say it’s bulletproof (you can certainly do stupid things with it if you want), but its much more foolhardy than the alternatives.

I have only been using Geneious for about 6 months, but it’s already indispensable. With the trend towards ever more data (particularly with next-generation sequencing), the case for such an integrated, user-friendly and transparent piece of software becomes clearer and clearer.