Hint: To do so, we start tree-puzzle in the same directory as the dataset - enter the dataset name when prompted for. To measure the phylogenetic content of a dataset switch the type of analysis to likelihood mapping ('b') and do not group the sequences. Start the mapping analysis typing 'y'.
Examine the result of the datasets in dataset-name.puzzle with a text editor and the likelihood mapping diagram dataset-name.eps (or with a postscript viewer like gsview.
Add the percentages in the corners to the the amount on completely resolved quartets. Summing the in the rectangles gives you the amount of partially resolved quartets. The percentage in the center gives the number of quartets which cannot be resolved. The last number should not be high.
Hint: We will examine this partial dataset on the Spanish Flu (South Carolina, 1918) from Worobey et al. (2002; DOI: 10.1126/science.296.5566.211a) using a 4-cluster likelihood mapping. Start tree-puzzle in the same directory as the dataset - enter the dataset name when prompted for. We switch the type of analysis to likelihood mapping ('b') and group sequences into 4 clusters ('g'):
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-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 Goldman et al. (2000; DOI: 10.1080/106351500750049752 and there are free copies found by google).
Hint: