SoftwareI've developed a number of tools in the course of research others may find useful.
- This package provides basic alignment tools to do pairwise alignment and set up and search a database of sequences with alignment. It is written in Ocaml
- PDB files contain information about proteins but are notoriously hard to handle. pdbread.ml is a library of routines designed to process these files and pdbtool is a command line utility for such tasks as sequence and coordinate extraction.
- Pre-release of Domo which does distance matrix analysis on proteins using semidefinite programming (see draft paper under my Research). The code for Domo is in two pieces. A modified version of the SDP solver CSDP was used in Domo. It must be downloaded and compiled. The main code for Domo comprises a series of Matlab files.