Software

PyML

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

TAPIS

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

iDiffIR predicts differential intron retention from RNA-seq data.

PAIRpred

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

SpliceGrapher

SpliceGrapher is a tool for predicting splice graphs and alternative splicing patterns using RNA-seq 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