Saturday, May 31, 2008

Software Review: Figtree a graphical tree viewer from Andrew Rambaut's Research Group

In spite of numerous noble efforts (e.g., TreeView, TreeEdit), the phylogenetics community has always lacked a simple, fully-featured application for viewing trees and their associated features. Figtree comes closer to meeting this need than anything that has come before. This program focuses exclusively on displaying trees and producing "publication-ready figures" and does not actually conduct any analyses (even things as simple as generating consensus topologies). Nevertheless, it has quickly become one of the most important tools in the phylogeneticist's box. It's easy-to-use graphical user interface permits users to do everything from selectively shading branches to displaying support values or branch lengths. Trees can then be exported to the PDF format, whether it be for publication or subsequent revision in a program like Adobe Illustrator. Although some users might have been hoping for exports in JPEG format, I'm glad this isn't included. JPEG files, of course, result from conversion of high quality vector graphics to compressed, rasterized graphics that are invariable of a lower quality than the originals. Nothing has done more to contribute to the hideous pixelated images that grace the pages of your favorite journals than the use of JPEG files (or other similar formats).


Aloysius Horn said...

FigTree is great. I love the ability to re-root and the export file format options. However I hope the next incarnation will allow one to display posterior probabilities from MrBayes 3.1 ".con" newick tree files. So far as I can determine it can't do this.

Glor said...

All you need to do to see these values is to click the "Node Labels" box and then choose "label" from the "Display" menu.

Aloysius Horn said...

Thanks, Glor!

Okay, now it's perfect!

Anonymous said...

I really like Fig Tree too, but am finding that consensus trees produced by PAUP cannot be re-rooted.

Do you know why this might be?