Are you looking for a fully featured program for the examination and analysis of DNA sequence data? Are you hoping for a way to avoid paying thousands of dollars for those über-annoying USB keys from Sequencher? The answer has arrived and it's name is Geneious.
Motivated by my desire to never purchase a single Sequencher key, I stumbled across this program when I was starting my lab a year or so ago. It was a revelation. Geneious' beautiful graphical user interface offered all of the Sequencher utilities I was looking to replace (e.g., viewing and editing of electropherograms, generation of contigs from individual sequencing runs). The only important feature that was missing when I first used Geneious was a function to identify potentially heterozygous positions, but, to my great surprise and delight, the Geneious developers added this feature within just a few days of my requesting it. This may be Geneious' greatest asset: a group of young developers who seem eager to respond to user requests and proactively expand their software's scope. Evolutionary biologists are particular lucky that Geneious' inventor - Alexei Drummond - is one of us.
As far as phylogenetic applications go, Geneious absolutely blows Sequencher out of the water. First, Geneious has some awesome features for visualizing aligned datasets (see figure). It also has a growing suite of built-in tree building algorithms. If you own a copy of the command line version of PAUP, you can use Geneious to implement analyses using PAUP's algorithms for Maximum Likelihood, Parsimony, and Neighbor-joining. Geneious will even run Modeltest for you before ML or NJ analyses (although it doesn't yet tell you which model it actually chooses, this is supposedly being fixed for the next release). Although users are permitted essentially limitless flexibility by inputting their own PAUP command blocks for these analyses, the same flexibility is not, unfortunately, provided in Geneious' application of MrBayes. At the present time, this application is limited to unpartitioned analyses with default parameter settings for variables such as temperature of the heated chains. Hopefully this feature will be upgraded in the near future.
If I have one remaining complaint about Geneious it is that it run frustratingly slow at times. Perhaps this is just an unavoidable outcome of trying to display so much data. Nevertheless, I've been running Geneious on fairly new OSX and WindowsXP machines (all with >2 GHz dual core processors and >2 GB of memory) and I'm not sure I'd try it with anything less.
In the final analysis, Geneious is not only an order of magnitude cheaper than Sequencher, it's also a better program. (Full disclosure: For the last few months, I've been a beta tester for Geneious and have been provided with one free license as a result. Having said this, I fell in love with this program long before receiving this perk and have put my money where my mouth is by purchasing two licenses for my lab.)
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