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New Review: CLC Workbench, Free Edition, and More

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Browsing the “internets”, I came upon new bioinformatics package called CLC Workbench. This is new at least for me: the site informs that more than 36000 users have downloaded the application. The program is developed by the Danish company CLC bio and they have some other nice products that I will mention in other posts.

I downloaded the free edition, the one that will give me everything for free and won’t put limits on this review. The order price for the full version is a hefty 4500 dollars, although you can rent the package monthly or purchase just a limited set of functionalities. The download went smoothly and installation was easy on my Fedora Core and XP boxes. As Geneious, CLC workbench is a Java application, and this is evident during the installation and first run. But Geneious interface, even though resembles a bit the “old” Java interfaces, looks cleaner and better designed than CLC Workbench.

On the first run on Linux, the program asks me if I want to download a example data set. Sure. It starts downloading and fails with an error message. There is an advance tab on the message but it does not work, the program seems frozen with a “Downloading data set” notice. I killed the process and I wondered why they did not include the data set with the download. The package is 25 Mb in size, a couple more won’t make a difference in high bandwidth times. I tried running again and no automatic message greeted me, so I decided downloading the data set manually. It failed again. I tried setting up the proxy and then searching NCBI: nothing.

I then moved back to my XP box and run the program. The same message greeted me and the this the download went smoothly. The interface is very similar on Linux and Windows, and the program’s approach is very similar to Geneious, as you have the same “feel” when running the program. There is no innovative GUI or analytical features on CLC Workbench, it is basically the same thing you see in other free packages. Basically you can align sequences, create extremely simple trees, analyse your DNA and protein and so on.

Most of its features overlaps with Geneious or BioEdit, and the late biOpen. Some random impressions on CLC Workbench:

  • alignment procedure extremely slow

  • interface is sometimes difficult to understand

  • it is hard to get used to double click on the left hand side toolbox

  • font size is large and clean

  • database search is fast and results are cleaner (visually) than Geneious

Based on the list above I would say that Geneious is better to the zero dollars you have to pay. It is good to see competition to Geneious, which I believe is gaining more ground in the market, especially due to its nice price for the registered version. I will test the paid versions of the other CLC’s software packages and post some reviews here.