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


TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) is a package for prediction and analysis of Pacific BioSciences Iso-Seq data. It performs error correction, splice isoform prediction, and prediction alternative polyadenylation sites. Results of running it in sorghum are available here


iDiffIR predicts differential intron retention from RNA-seq data.


PAIRpred: prediction of protein-protein interfaces from sequence and structure.


SpliceGrapher is a tool for predicting splice graphs and alternative splicing patterns using RNA-seq data, guided by gene models and EST data.


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


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