After reviewing Geneious twice, I decided to search for other proprietary software that would be comparable in price, features and capabilities. I happened to find such software: biOpen, from a French company called AbOrygen.
biOpen motto is “Simply modular”, and in this case the modules come from where they should: the company that makes the software. If I am paying a considerable amount of money for a program that will help me do my research, I want any module/plugin to be reliable and take full advantage of the base program. AbOrygen’s website mentions that they have plans to release a SDK for biOpen, but no word on availability or features.
In a full comparison, biOpen lacks some of the eye catching details of Geneious, a little bit the ease of use and some functionality regarding PubMed searches. But biOpen does have some advantages if you are interested in doing actual science and do not care for the latest trend in design. Also, biOpen is a Mac only application, hence its interface using the Mac-favourite approach of a multi-window GUI (they claim a Windows and Linux version are coming). Basically the program has main project window, an analysis window and a small log, that can be scattered around on your desktop. The analysis is based on projects, not on folders as Geneious, and the data is organized as such.
On the scientific side, biOpen excels: contig assembly, vector cleaning, ORF search, PCR and other neat features for DNA/RNA/protein analysis. But the best is their pairwise/multiple alignment suite of programs that allows you to align your sequence with ClustalW (OK), Muscle (good) and ProbCons (excellent). The latter is one of the best programs to align proteins available (see here) and it is much better than the reliable old-timer ClustalW. On the other hand, on Geneious you are stuck with ClustalW and a proprietary alignment algorithm that no one tested, or maybe you will be waiting for some good heart develop a plugin that will allow the use of better alignment packages.
Also, by being “simply modular”, you can order only the modules you want, whenever you want. You can get biOpen for a spin before buying. If you are more interested on doing hard-core research, this is a very strong competition to Geneious. And if you are interested in having a GUI for two of the best programs for sequence alignment you definitely would give biOpen a try.