EvidentialGene : Evidence Directed Gene Construction for Eukaryotes

2024 Aug : Gnodes #2 doc: the long & short of it ...
2023 Dec : Gnodes #3, Holiday Genomics Puzzle
2023 Jul : Gnodes major contents in animal and plant genomes
2022 May : Gnodes #1 publication is now available
2021 Feb : Genome Depth Estimator for animals & plants
2020 Dec : Daphnia species genomes 2020 update
2020 Mar : EvidentialGene major update
2019 Oct : Gene Reconstruction Filters draft paper
2019 May : SRA2Genes Test Drive
2019 Mar.: eugenes.org moved to jetstream indiana and google iowa farms
2018 Jul.: Evigene 2018 of Sus scrofa pig
2018 Jan.: Animal & Plant Evigene constructions surpass NCBI, Ensembl, Maker, PacBio and Trinity methods for Arabidopsis, Corn, White fly, Water flea, Zebrafish
2017 Dec.: Evigene 2017 of Danio rerio zebrafish
2017 Dec.: Evigene 2017 of Lytechinus variegatus green sea urchin
2017 Nov.: Evigene 2017 genes of Daphnia pulex water flea
2017 June: Evigene set for Bemisia tabaci whitefly crop pest
2017 May : Evigene set for Arabidopsis th. model plant
2016 : Evigene gene sets for Zea mays corn plant, Anopheles and Aedes mosquitos, and Pine trees
2015 : Evigene gene-ome set for Daphnia magna , and for Atlantic Killifish
2014 : EvidentialGene sets are Best of clade in gene set completeness for Arthropods, Plants and Fishes .
2014 : Evigene gene-ome sets for Honey Bee, Deer Tick, and Tribolium Beetle are publicly available.

 Name                    Last modified       

 Parent Directory        23-Apr-2019 15:32  
 about/                  25-Jan-2023 12:42  
 arthropods/             14-Mar-2021 16:09  
 daphnia/                12-Jun-2023 21:42  
 evigene/                14-Aug-2022 12:41  
 inverts/                14-Dec-2017 17:23  
 other/                  23-Feb-2021 22:12  
 plants/                 21-May-2017 19:09  
 vertebrates/            25-Mar-2019 14:06

Folder evigene/ contains this software, about/ describes this work, in posters and documents. Evigene software archives, best way to fetch, are in /EvidentialGene/other/evigene_old/. The other folders contain gene-ome sets of animals and plants, constructed with EvidentialGene software. Some of these are chromosome-free, others are mixed chromosome-guided and mRNA-assembled.

See also EvidentialGene @ Sourceforge.net and ask questions, discuss at EvidentialGene @ Google Groups

2016: EvidentialGene Explained at Galaxy & GMOD conference, 2016 June
EvidentialGene mRNA Transcript Assembly Software
2013: Gene-omes built from mRNA-seq not genome DNA
Evigene-mRNA
Independent comparison of EvidentialGene_trassembly doi: 10.1371/journal.pone.0091776
2012: Perfect Genes Constructed with Gigabases of RNA

EvidentialGene Animal & Plant Genes Quality Comparison

EvidentialGene : Evidence Directed Gene Construction for Eukaryotes

EvidentialGene comes in two flavors, Evigene-G following the genome-gene modeling paradigm, and Evigene-R following the gene assembly from RNA paradigm (see Evg-G/R workflow figures 1A,1B): Evigene-G algorithm is summarize at Perfect Genes Constructed with Gigabases of RNA . Evigene-R algorithm is summarize at Gene-omes built from mRNA-seq not genome DNA . Development of Evigene-H hybrid of the two is in progress.

Don Gilbert, gilbertd at indiana edu home at http://eugenes.org/EvidentialGene/

Evigene-G and Evigene-R Pipelines Workflow Summary

Evigene-G Workflow Details

Developed at the Genome Informatics Lab of Indiana University Biology Department