  In many experiments, the aim is to deduce an underlying multi-substate on-off
kinetic scheme (KS) from the statistical properties of a two-state trajectory.
However, the mapping of a KS into a two-state trajectory leads to the loss of
information about the KS, and so, in many cases, more than one KS can be
associated with the data. We recently showed that the optimal way to solve this
problem is to use canonical forms of reduced dimensions (RD). RD forms are
on-off networks with connections only between substates of different states,
where the connections can have non-exponential waiting time probability density
functions (WT-PDFs). In theory, only a single RD form can be associated with
the data. To utilize RD forms in the analysis of the data, a RD form should be
associated with the data. Here, we give a toolbox for building a RD form from a
finite two-state trajectory. The methods in the toolbox are based on known
statistical methods in data analysis, combined with statistical methods and
numerical algorithms designed specifically for the current problem. Our toolbox
is self-contained - it builds a mechanism based only on the information it
extracts from the data, and its implementation on the data is fast (analyzing a
10^6 cycle trajectory from a thirty-parameter mechanism takes a couple of hours
on a PC with a 2.66 GHz processor). The toolbox is automated and is freely
available for academic research upon electronic request.
