wiki/genetreepreprocessing.wiki

   1 #summary preprocessing of gene trees for speciation/duplication inference
   2
   3 = Gene tree preprocessing =
   4
   5 == Purpose ==
   6
   7 Use EBI database to add species information to a gene tree which has sequence identifiers as labels.
   8
   9 == Usage ==
  10 {{{
  11 java -Xmx1024m -cp
  12 path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
  13 }}}
  14
  15
  16
  17 == Details ==
  18
  19 Output consists of three files:
  20   * input-name_preprocessed_gene_tree.phylo.xml
  21   * input-name_species_present.txt
  22   * input-name_removed_nodes.txt
  23
  24
  25 == Download ==
  26
  27 Download forester.jar here: http://code.google.com/p/forester/downloads/list