Zientzilaria

Covering the bioinformatics niche and much more

Geneious and "Specialized" Software, Featuring Dendroscope

| Comments

Last week a new phylogenetic tree viewing program was released/published. Called Dendroscope it is a very nice piece of software that has lots of useful features to view, edit and manipulate phylogenetic trees.

Its release/publication coincided with a period in the lab when two of the graduate students were obtaining new results, especially in the form of phylogenetic trees. There was some debate whether TreeView should be used, but we couldn’t compile for all Linux boxes we have, due to differences in their distro version. So, at first we checked Geneious, which has been reviewed here, and it is a do-it-all phyloegenetic/molecular biology/name-it software. Geneious has some very nice features, but I cannot call its tree viewing option excellent. Let’s say good defines it more than enough.

One particular nagging thing included in Geneious’ latest releases were some extra features to expand/collapse branches, which are circles drawn over the tree’s nodes. One cannot turn off these circle, they are always there and sometimes with different diameters. When I first saw them I though it was showing some kind of support for the node but I was wrong. After some fidgeting we discovered that circles can be turned off, but only when you are exporting/printing the tree.

Bringing back Dendroscope. Intuititve interface, it delivers what you want and more than you expect for a tree viewing program. After one hour of playing one of the graduate students was already a pro-user of the software, showing everyone what can be accomplished with Dendroscope. And yes, there are no deceiving circles on the nodes. As Geneious, it is a Java based application, so easy to port to different systems. But differently it does one thing and does it better than the “competition”. That makes me question myself: why should you leave your “specialized” applications in favour of Geneious when the end product is below your expectation?

Maybe because of the competition Geneious got away of its almost sure path to be the “holy grail” of phylogenetics/molecular biology software. Trying to embrace every aspect of research at once might take its toll on the simpler details that are still not fixed/changed in the program. When Geneious was released it had the right amount of features and, as any other software, a little bit buggy but it delivered what you wanted. The program grew considerably since its first inception and it can do mostly of the common tasks of a small-medium biology lab requires in a day. Still, why would you want to trade your reliable do-one-thing-do-it-better application in favour of a do-it-all-do-it-so-so program that might have tons of features you will never use? Yep, I find a lot of things in MS Word that I don’t need, that’s why I use e, TextMate, Notepad++. And for tree viewing I will dump my always-loved TreeView and adopt the new kid on the block, Dendroscope.