Software

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

Title Description Software
E2P2 version 1 Ensemble-based Enzyme Prediction Program (E2P2) version 1 is a program that predicts metabolic enzymes in a sequenced genome. [Publication] [README] E2P2V1
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
miP3 version 1 microProtein Prediction Program (miP3) version 1 is an algorithm that predicts microProteins in a sequenced genome. [Publication] [README] miP3V1
miP3 version 2 microProtein Prediction Program (miP3) version 2 predicts microProteins in a sequenced genome. It is more streamlined and simplified than version 1 and can be used by biologists without the need to install programs locally. [Publication] [README] miP3V2