One of the irritating jobs during DNA analyses is often the preparation for input files for different programs. Although the Nexus-format is becoming a standard more and more, some older programs require different formats, e.g. Newick or Phylip. While most programs are very forgiving for the type of input (interleaved or not), some are very strict in their requirements.
For several reasons I liked to try the program TreePuzzle (www.tree-puzzle.de). This program requires all input files in the interleaved Phylip format, so I set up CLUSTALW to export my alignment in that format. As the Phylip format only allows 10 positions for the taxon name, I had to manually edit these names to remain meaningful to me.When I had overcome this hurdle, the program runs in a Terminal window and allows various options to be set.
One of the options allows likelihood mapping. This is based on quartet puzzling and produces a graphical output indicating the number of resolved and conflicting quartets as percentage.
In my data set the percentage resolved quartets is 95.5%, which seems sufficiently high to explore the data further.
Likely to be continued.