This page lists and makes available the programs we have developed in our lab.

Title Description Software
E2P2 version 3.1 E2P2 version 3.1 fixes a couple of bugs [README] E2P2V3.1
E2P2 version 3.0 E2P2 version 3.0 includes expanded reference enzyme sequence libraries updated versions of component software packages. Additional updates were made to improve prediction performance detailed more in the README file. [README] E2P2V3.0
E2P2 version 2.1 E2P2 version 2.1 includes expanded reference enzyme sequence libraries and improved performance assessment and base classifier integration schemes. [README] E2P2V2.1
SAVI version 3.02 Semi-Automated Validation Infrastructure version 3.02 processes predicted metabolic pathways using pathway meta data such as taxonomic distribution and key reactions and makes decisions about which pathways to keep, remove, and subject to manual validation. [README] SAVIV3.02
PlantClusterFinder version 1.0 A pipeline to predict metabolic gene clusters from plant genomes [README] PlantClusterFinder1.0
PlantClusterFinder version 1.2 An updated version of Plant Cluster Finder to handle species with complex GeneID to ProteinID mappings [README] PlantClusterFinder1.2
PlantClusterFinder version 1.3 A major update with improved user friendliness and easier interpretation of results [README] [Release Notes] PlantClusterFinder1.3
miP3 version 2 microProtein Prediction Program (miP3) version 2 predicts microProteins in a sequenced genome. It is more streamlined and simplified than version 1. [README] miP3V2
GRACE GRACE (Gene Regulatory network inference ACcuracy Enhancement) is an algorithm that enhances the accuracy of transcriptional gene regulatory networks by using a Markov Random Field approach. [README] GRACE