  This chapter discusses the way in which dimensionality reduction algorithms
such as diffusion maps and sketch-map can be used to analyze molecular dynamics
trajectories. The first part discusses how these various algorithms function,
as well as practical issues such as landmark selection and how these algorithms
can be used when the data to be analyzed, comes from enhanced sampling
trajectories. In the later parts, a comparison between the results obtained by
applying various algorithms to two sets of sample data is performed and
discussed. This section is then followed by a summary of how one algorithm, in
particular, sketch-map, has been applied to a range of problems. The chapter
concludes with a discussion on the directions that we believe this field is
currently moving.

Computational Physics;Statistical Mechanics