Quick start
- Start the executable file.
- Go the preference window (edit, preferences) and set the
following paths:
- treeviewer 1 (should be Treeview, because only Treeview (to
our knowledge) is able to deal with several trees at once)
- treeviewer 2 (should be NJplot, because for large trees
NJplot is able to zoom in subtrees)
- rate matrix (in the example folder you will find to example
matrices specific for the example data)
- load your sequence data (in the example folder you will find
some examples (e.g. artificial.fas, chloro.fas))
- press the run button
- press the tree button
- 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)
- the first tree will show you the distance tree, the second one
shows the corresponding consensus tree
- if ProfDist performed more than one iteration scroll through all
PNJ trees
- edit carefully the PNJ driving threshold parameters (percent
identity and minimal bootstrap value (also in percent)) in the preferences
section and start again