Hint:
Hint: We start tree-puzzle in the same directory as the dataset - enter the dataset name when prompted for, and the treefile as well later. To test trees on a dataset switch the tree search procedure to evaluate user defined trees ('k'). Change option to use neighbor-joining tree ('x') for parameter estimation. Start the analysis by typing 'y'.
Examine the results in flu-a-full.phy.puzzle or flu-a-1000.phy.puzzle with a text editor. At the end is a table of results from three different tests (Kishino-Hasegawa test, Shimodaira-Hasegawa test, Expected Likelihood Weights) containing all the trees, with those being marked by '-' which are significantly worse than the best tree while those with '+' are not.
There is a good overview and discussion on testing trees by Golman et al. (2000; DOI: 10.1080/106351500750049752 and there are free copies found by google).