A detailed description of all tools is available in the AnnoTALE User Guide_.

**TALE Class Builder** Clusters a set of input TALEs into a number of classes.

For clustering, TALEs are aligned by the RVD sequences, where mismatches at position 12 of a TALE are penalized with a value of ``0.2`` and mismatches at position 13 are penalized with a value of ´´0.8´´. The alignment distance of two TALEs is then the sum of the penalties in the alignment between these two TALEs. Clustering is performed with agglomerative hierarchical clustering using average linkage.

The input of *TALE Class Builder* are a set of TALE DNA sequences (as obtained from the *TALE Prediction* tool), the *Cutoff* that defines the maximum distance of TALEs in a class (i.e., the larger this value, the larger the classes will be), and the *Significance level* for the p-values of alignments of TALE sequences.

The output of *TALE Class Builder* is a report and a graphical representation for each of the classes, a tree representing similarity of TALE classes, and a ``Class builder`` definition that may serve as input of the *TALE Class Assignment* tool.

If you experience problems using *TALE Class Builder*, please contact_ us.

.. _contact: mailto:grau@informatik.uni-halle.de
.. _AnnoTALE User Guide: http://www.jstacs.de/downloads/AnnoTALE-UserGuide-1.0.pdf