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Quick start

  1. Start the executable file.
  2. Go the preference window (edit, preferences) and set the following paths:
    1. treeviewer 1 (should be Treeview, because only Treeview (to our knowledge) is able to deal with several trees at once)
    2. treeviewer 2 (should be NJplot, because for large trees NJplot is able to zoom in subtrees)
    3. rate matrix (in the example folder you will find to example matrices specific for the example data)
  3. load your sequence data (in the example folder you will find some examples (e.g. artificial.fas, chloro.fas))
  4. press the run button
  5. press the tree button
  6. scroll through all estimated trees by clicking to the upper left arrows (only in treeview!), otherwise you have to edit the trees in the output window of ProfDist (only the first tree is shown by typical treeviewers like NJplot or hypergeny)
  7. the first tree will show you the distance tree, the second one shows the corresponding consensus tree
  8. if ProfDist performed more than one iteration scroll through all PNJ trees
  9. edit carefully the PNJ driving threshold parameters (percent identity and minimal bootstrap value (also in percent)) in the preferences section and start again