Software Tools

Title
Description
Software
E2P2 version 5
E2P2v5 adds the ability for users to define their own classifiers and swap them out, and replaces PRIAM with DeepEC as a default classifier [README]
E2P2v5
E2P2 version 4
​Allows the use of external BLAST and PRIAM rather than versions packaged with E2P2. Moved project to Github. [README]
E2P2v4
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
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
Genome Annotation Status
A web app to graphically visualize status of genome function annotation for model species and select bioenergy & food crops.
GenomeAnnotation
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
​PlantClusterFinder version 1.3
​A major update with improved user friendliness and easier interpretation of results [README] [Release Notes]
PlantClusterFinder1.3
PlantClusterFinder version 1.2
An updated version of Plant Cluster Finder to handle species with complex GeneID to ProteinID mappings 
PlantClusterFinder1.2
PlantClusterFinder version 1.0
A pipeline to predict metabolic gene clusters from plant genomes 
PlantClusterFinder1.0
QTG-Finder2
​A generalized machine learning algorithm to prioritize causal genes in quantitative trait loci for any plant species. [README]
QTG-Finder2
​QTG-Finder version 1.1
A machine learning algorithm to prioritize causal genes in quantitative trait loci. [README]
QTG-Finderv1.1
SAVI version 3.2
​SAVI 3.2 contains minor changes to make scripting easier, and updated validation lists for PMN 16 ​[README]
SAVIv3.2
SAVI version 3.1
​SAVI 3.1 contains bug fixes, an improved README, and updated validation lists for PMN 14 [README]
SAVIv3.1
​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
Unigene finder (NEW)
UnigeneFinder is an automated pipeline designed to simplify and improve gene prediction from de novo transcriptome assemblies​, especially for non-model organisms that lack a reference genome.
Unigene v1.0
STANFORD & MICHIGAN STATE UNIVERSITY LAND ACKNOWLEDGEMENTS
“Stanford sits on the ancestral land of the Muwekma Ohlone Tribe. This land was and continues to be of great importance to the Ohlone people. Consistent with our values of community and inclusion, we have a responsibility to acknowledge, honor, and make visible the University’s relationship to Native peoples.”
"We acknowledge that Michigan State University occupies the ancestral, traditional, and contemporary Lands of the Anishinaabeg – the Three Fires Confederacy of Ojibwe, Odawa, and Potawatomi peoples. We affirm Indigenous sovereignty and hold Michigan State University accountable to the needs of American Indian and Indigenous peoples."