Software

PyML

PyML is an interactive object oriented scripting framework for machine learning written in Python. PyML focuses on SVMs and other kernel methods.

SpliceGrapher

SpliceGrapher is a tool for predicting splice graphs and alternative splicing patterns using next generation sequencing data, guided by gene models and EST data.

MI1

MI1 is a method for predicting Calmodulin binding sites. We have created an online tool that biologists can use to obtain predictions for their proteins

Strut

Strut is a C++ package for structured large-margin classification that is designed for hierarchical classification problems such as protein function prediction.

DAWGS

DAWGS is a library implementing directed acyclic word graphs, which are data structures that allow efficient search for all substrings that occur within a given string. It also provides a method for discovery of k-mers-with-mismatches that discriminate between two sets of sequences