wiki/genetreepreprocessing.wiki

   1 = Gene tree preprocessing =
   2
   3 == Purpose ==
   4
   5 Use EBI database to add species information to a gene tree which has sequence identifiers as labels.
   6
   7 == Usage ==
   8 {{{
   9 java -Xmx1024m -cp
  10 path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
  11 }}}
  12
  13
  14
  15 == Details ==
  16
  17 Output consists of three files:
  18   * input-name_preprocessed_gene_tree.phylo.xml
  19   * input-name_species_present.txt
  20   * input-name_removed_nodes.txt
  21
  22
  23 == Download ==
  24
  25 Download forester.jar here: http://code.google.com/p/forester/downloads/list