Phyutility (fyoo-til-i-te) is a command line program that performs simple analyses or modifications on both trees and data matrices. Makes use of JADE (PEBLS) and JEBL libraries. Please see the NEWS page for info concerning updates, etc.

Please use this citation when using Phyutility Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24: 715-716

Currently it performs the following functions (to suggest another feature, submit an Issue and use the label Type-Enhancement) :

Trees

• rerooting
• pruning
• type conversion
• consensus
• leaf stability
• lineage movement
• tree support

Data Matrices

• concatenate alignments
• genbank parsing
• trimming alignments
• search NCBI
• fetch NCBI

please reroot your trees before performing the leaf stability, lineage movement, or consensus functions -- unrooted functions for these will be incorporated ASAP

07-04-2009 Uploaded new .jar file for phyutility. Please download this and replace your existing phyutility.jar file (of course, if yours is named Phyutility.jar, change the name of the new file to reflect that). If you haven't downloaded phyutility package before, please download both and replace the .jar in the folder with the new one. More features soon!