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README.md

phyutility

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.

See [NEWS] and download the new release for amino acid acceptance in the concatenate and cleaning functions (use the -aa argument in -clean and -concat functions).

Please use this citation when using Phyutility [http://bioinformatics.oxfordjournals.org/cgi/content/short/24/5/715 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

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