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