PNJ reads FASTA- or EMBL format (INPUT).
PNJ calculates in an iterative way ([18] phylogenetic trees given in NEWICK format (OUTPUT).
The resulting phylogenetic trees can be viewed and edit in your preferred treeviewer (the path is set in the preferences window 4.6). Trees show not only bootstrap values but also nodes specified uniquely by numbers, e.g. 13.85 means that at node 13 a bootstrap value of 85 occurred. Note that the tool treeview is able to deal with several trees in contrast to NJplot and other treeviewers. This means in particular that only treeview is able to scroll through all trees calculated in each iteration.
In the preferences section window, the essential parameters of PNJ are shown and can be set or adjusted:
- the number of bootstrap replicates,
- the distance estimation method
- a user defined substitution model,
- the PNJ agglomeration procedure
- 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 the profile neighbor joining algorithm there are only two driving parameters important:
- the minimal bootstrap value supporting a group of sequences representing a trustworthy monophyletic group which is transformed to a sequence profile, and
- a percent identity threshold representing an a priori profile to prevent low bootstrap values due to high sequence identities.
PNJ runs in four different modi:
- automatic default
- half automatic (first step)
- half automatic (every step)
- manual
Note that clearly every single sequence is a very special case of a sequence profile,
as well as that automatic generated profiles are often (automatically) summarized into a new profile.
For a more detailed description of the latter three modi two, three and four please read the chapter ?? below.
Here are some examples of automatic generated profiles:

Figure 4.1: At node 32 a profile is generated because all nodes to the right and to the left have bootstrap values higher than a certain threshold given in the preferences window (in this case 90).

Figure 4.2: All sequences of the subtree associated to node 47 are summarized to a profile. The remaining sequences Schizomeris leibleinii and Aphanochaete magna are handled as two profiles because the bootstrap values at the node 46 is below the given threshold. This is also the reason that although there is a high bootstrap value at node 45 no profile is generated at this node.

Figure 4.3: At node 37 a profile is generated although the bootstrap value at node 38 is below the threshold. The profile is generated due to the high level of sequence identity (percent identity threshold ) of both sequences Sphaeroplea robusta and Spaeroplea soleirolii v crassiseptra (99.8 %).

Figure 4.4: Starting Window of ProfDist. Beside File, Edit, Functions and Help you see buttons like open, save, undo, copy, cut, paste, run, treeview, preferences and help as well as the starter buttons of the programs Bootstrap, Distance, Neighbor-Joining, Consense and Profile Neighbor-Joining.

Figure 4.5: Starting Window of ProfDist with closed input window. If you load large datasets it is convenient to close the input window by disabling the checkmark input window on the right hand site of the input window.

Figure 4.6: Preferences window.

Figure 4.7: Preferences window with expert settings.

Figure 4.8: Organisms classification window. Here you can edit the (profile) taxon sampling.