Software
	Legend: =gene finder; =open source; =related program or software
	Project				Description		Contacts
	mGene				GHMM / SVM eukaryotic gene finder		Gunnar Raetsch
	SNAP				GHMM eukaryotic gene finder		Ian Korf
	GeneZilla (formerly TIGRscan)				GHMM eukaryotic gene finder		Bill Majoros
	GlimmerHMM				GHMM eukaryotic gene finder		Mihaela Pertea
	TWINSCAN				GHMM informant method for comparative gene finding		Michael Brent
	ChemGenome				prokaryotic, ab initio gene finder based on physico-chemical properties		Shailesh
	TWAIN				GPHMM comparative gene finder		Bill Majoros
	ExoniPhy				Phylogenetic HMM gene finder		Adam Siepel, David Haussler
	Shadower				Generalized Hidden Markov Phylogeny (GHMP) gene finder		Michael Jordan
	JIGSAW (formerly "Combiner")				Evidence combiner for eukaryotic gene prediction		Jonathan Allen
	GenomeThreader				Similarity-based gene prediction program where additional cDNA / EST and/or protein sequences are used to predict gene structures via spliced alignments.		Gordon Gremme
	EvoGene				Evolutionary HMM gene finder		Jakob Pedersen
	ExonHunter				Integrative gene finding system		Broňa Brejová
	GlimmerM				Eukaryotic gene finder using OC1 decision trees and Interpolated Markov Models.		Mihaela Pertea
	Unveil				HMM eukaryotic gene finder		Bill Majoros
	Glimmer				Prokaryotic gene finder using Interpolated Markov Models		Art Delcher, Steven Salzberg
	CRITICA				Comparative prokaryotic gene finder		Jonathan Badger
	SGP2				Comparative gene finder based on geneid and TBLASTX		Genis Parra, Josep F. Abril, Roderic Guigó
	Phat				GHMM gene finder		Simon Cawley
	geneid				Hierarchically-structured gene prediction program		Enrique Blanco, Roderic Guigó, Genis Parra
	SLAM				Pair GHMM-based syntenic gene finder		Lior Pachter
	EuGene				An open gene finder for eukaryotic organisms		EuGene Team
	GENSCAN				GHMM-based gene finder for human		Chris Burge
	AUGUSTUS				GHMM-based gene finder for eukaryotes		Mario Stanke
	SGP1				Similarity based gene prediction program		Roderic Guigó
	VEIL				HMM eukaryotic gene finder (no longer supported)		John Henderson, Steven Salzberg
	MORGAN				A eukaryotic gene finder using OC1 decision trees (no longer supported)		Steven Salzberg, Art Delcher
	GenomeScan				GHMM informant-based gene finder		Chris Burge
	DoubleScan				Pair HMM gene finder		Irmtraud Meyer
	HMMgene				HMM gene finder		Anders Krogh,  Kristoffer Rapacki
	GRAIL				Neural-network-based gene-finder		grailmail@ornl.gov
	GrailEXP				Neural-network-based gene finder (Oak Ridge Natl. Lab.)		feedback.cfm
	Genie				GHMM-based gene finder		David Kulp, Martin Reese
	GeneMark(tm)				a gene finder from Georgia Institute of Technology		Mark Borodovsky
	FGENESH				GHMM gene finder		softberry@softberry.com
	ORPHEUS				bacterial gene finder		Grigori Kolesov
	PROCRUSTES				gene finder utilizing protein evidence		Pavel Pevzner
	Diogenes				searching for and reporting likely protein-encoding regions		John A. Crow
	WebGene				Tools for prediction and analysis of protein-coding gene structure
	GeneSplicer				A fast, flexible system for detecting splice sites in eukaryotic DNA.		Mihaela Pertea
	ORF Finder				program at NCBI to find ORFs in a sequence		Tatiana Tatusov,  Roman Tatusov
	SplicePredictor				a method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models
	NetPlantGene				neural network predictions of splice sites in Arabidopsis thaliana DNA		Søren Brunak, Pierre Rouze
	NetGene2				neural network predictions of splice sites in human, C. elegans and A. thaliana DNA		Søren Brunak
	ELPH				Gibbs sampler for finding motifs in DNA; has been used for detecting exon splice enhancers (ESE's).  Also applicable to other motif-detection tasks.		Mihaela Pertea
	RBSfinder				A program to find ribosome binding sites in prokaryotic DNA.		Steven Salzberg
	TransTerm				A program that finds rho-independent transcription terminators in bacterial genomes		Maria Ermolaeva
	OC1				oblique decision trees for classification		Steven Salzberg, Simon Kasif
	TAIL				machine-learning library: neural nets, decision trees, multivariate regression, Bayesian classifiers, genetic algorithms/genetic programming, and K-nearest-neighbors with feature selection and correlation control		Bill Majoros
	wotd				suffix trees		Stefan Kurtz
	tigr++				C++ class library used by several TIGR genefinders and other packages.  Covers string & sequence processing, math/statistics, many efficient data structures, GFF parsing, sorting, and I/O.		Bill Majoros
	PROSCAN/ PromoterScan				Predicts promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences		Dan Prestridge

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