- GENEID – A program to predict genes, exons, splice sites and other signals along a DNA sequence.
- AUGUSTUS – Program that predicts genes in eukaryotic genomic sequences.
- EuGene – Integrative gene finder for eukaryotic and prokaryotic genomes.
- PseudoPipe – A stand alone computational pipeline for pseudogene annotation.
- GenScan – Web server for the identification of complete gene structures in genomic DNA.
- HMMgene – 1.1 – Program for prediction of vertebrate and C. elegans genes.