Note: If you are using Excel to edit GenePattern files, be sure to save the file as a tab-delimited text file and supply the correct file extension. You can specify the file name in quotes to prevent Excel from appending .txt to the file name. Also, note that Excel's auto-formatting can introduce errors in gene names, as described in Zeeberg, et al (2004).
GTR File Format
GTR files will be created by the HierarchicalClustering module. This is a format defined at Stanford for their Hierarchical Clustering program. Note that the HierarchicalClustering module will also generate a CDT file.
The GTR (gene tree) file records the order in which the genes (rows) were joined during clustering.