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General features

In the preferences section window, the essential parameters of PNJ are shown and can be set or adjusted:
  1. the number of bootstrap replicates,
  2. the distance estimation method,
  3. a user defined substitution model,
  4. the PNJ agglomeration procedure and
  5. the path to the preferred tree viewer.
Implemented distance estimation methods are JC [12], K2P [13], GTR [14], [15] or the Log-Det transformation [16]. For both distance estimation methods based on the GTR model it is essentiell that a substitution matrix is already loaded in the preferences window. Two example models (Q_chloro.txt, Q_arthro.txt) are given in the example folder in PNJ.

For the profile neighbor joining algorithm there are only two driving parameters important:

  1. the minimal bootstrap value supporting a group of sequences representing a trustworthy monophyletic group which is transformed to a sequence profile, and
  2. a percent identity threshold representing an a priori profile to prevent low bootstrap values due to high sequence identities.
In the preferences window you can set the path to your preferred treeviewer tool (see Figures 4.6,4.7). This treeviewer is activated later on using the tree button mentioned above.