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In many experiments, the aim is to deduce an underlying multi-substate on-offkinetic 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 ofinformation about the KS, and so, in many cases, more than one KS can beassociated with the data. We recently showed that the optimal way to solve thisproblem is to use canonical forms of reduced dimensions (RD). RD forms areon-off networks with connections only between substates of different states,where the connections can have non-exponential waiting time probability densityfunctions (WT-PDFs). In theory, only a single RD form can be associated withthe data. To utilize RD forms in the analysis of the data, a RD form should beassociated with the data. Here, we give a toolbox for building a RD form from afinite two-state trajectory. The methods in the toolbox are based on knownstatistical methods in data analysis, combined with statistical methods andnumerical algorithms designed specifically for the current problem. Our toolboxis self-contained - it builds a mechanism based only on the information itextracts from the data, and its implementation on the data is fast (analyzing a10^6 cycle trajectory from a thirty-parameter mechanism takes a couple of hourson a PC with a 2.66 GHz processor). The toolbox is automated and is freelyavailable for academic research upon electronic request.

Toolbox for analyzing finite two-state trajectories