A collection of general purpose functions of broad applicability that form an infrastructure for other toolboxes. These functions accept standard arguments as inputs, and produce standard arguments as outputs, thus making no use of objects defined in my other toolboxes.

This toolbox allows for analysis of any form of multivariate data. Specifically, it is designed to cope with the three standrad forms of data matrices: a variable-by-sample matrix (e.g., gene array), a sample-by-sample matrix (e.g., distance matrix), and a variable-by-variable matrix (e.g., correlation matrix). Roughly, the toolbox allows for visualization of such data, for dimensionality reduction and for classification (discriminant analysis).

This toolbox is not as developed as the multivariate analysis toolbox. It allows for limited analysis of multiple alignments, and a reasonable analysis of phylogenetic trees.

An algorithm for parameter estimation and ancestral reconstruction of the evolution of binary characters.

An algorithm for reconstruction genome-wide, high-resolution, methylation patterns along ancient DNA. The newest version is available at GitHub.

The code to identify differential DNA methylation in non-skeletal tissues is avaialble here as a Matlab script.