AAT - Analysis and Annotation Tool from Michigan Tech University is used to identify genes by comparing cDNA and protein sequence databases.
ABI PRISM software products, from Applied Biosystems, provide advanced, automated analysis for the range of genetic analysis applications from fragment sizing to database matching to pedigree drawing.
AcaClone pDRAW32 is a freeware DNA cloning, analysis and visualisation software
AGCT Hybridization simulation and oligo analysis software especially suited for diagnostic, therapeutic, and common gene family research
AlleleID designs probes and primers for pathogen detection, bacterial identification, species identification and taxa discrimination using qPCR and microarray assays
Antheprot Protein analysis software
Array Designer 4: Design efficient, specific oligos for SNP genotyping and expression microarrays
arraySCOUTTM is a gene expression data analysis application
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features
Ancestor,designed to inferace ancestral amino acid sequence from set of homologous amino acid sequence whose phylogent relation is known
Asterias is a suite of freely- accessible web-based genomic data analysis programs
Beacon Designer 6: designs oligos for SYBRŽ Green, TaqManŽ, LNA spiked TaqManŽ, MethyLight, molecular beacon, NASBAŽ and FRET assays
Bio Image is a life sciences software information company which carries a wide variety of electrophoresis image analysis software for Windows, Powermac, and UNIX
BioinformatiX is an enterprise software which provides an environment for the analysis of microarray data
BioRainbow Analysis Tools are a collection of software tools for binding site prediction, weight matrix search, regulatory sequences analysis, microarray analysis, footprint
bioSCOUT is a comprehensive and customizable bioinformatics package
BioTools offers three primary bioinformatics products: GeneTool for DNA sequence analysis, PepTool for protein sequence analysis, and ChromaTool for chromatogram analysis
BlockSearch is a quantitative method for the elucidation of unknown protein function
Clann: Software for investigating phylogenomic information using supertrees
CLC Free Workbench is a freeware bioinformatics software package
CURVES, by Richard Lavery and Heinz Sklenar is a very useful nucleic acid helical analysis program
DisTree it computes pairwise distance of allied nucleotide sequence utilizing various models of base substitution.
DNADynamo is a general purpose software for DNA and Protein sequence analysis
DNASIS is a robust sequence analysis software package
DNPTrapper is a shotgun sequencing assembly editing tool, specifically designed for finishing and analysis of repeated regions
EuGene and SAm is a menus based DNA and protein sequence analysis package
Expression is a powerful application for DNA and protein sequence analysis
Genchek , developed by Ocimum Biosolutions is a comprehensive, LIMS based, user friendly Nucleotide and Polypeptide Sequence Analysis Tool
Genehound offers a new, innovative, and exciting apporach to identifying coding regions in prokaryotic genomes
GeneInform is an easy-to-operate gene expression management and analysis tool
Gene Inspector1.5: A powerful and versatile combination of an electronic laboratory notebook and sequence analysis package for biologists
GeneJockey is a program for editing, manipulation, and analysis of nucleic acid and protein sequences
GeneLinker products are the easiest way for researchers to start analyzing gene expression data
GENEMARK is a genefinding tool
GENEPARSER is a coding region recognition program
GeneSifter, a Web-based microarray analysis system that combines data management and analytical functions with integrated, current gene annotation
GeneSolve is a single-User desktop sofware package for analyzing nucleic acid sequence infromation
GeneWorks - an integrated sequence analysis and database searching(http://www.genestudio.com/) is a newly developed suite of molecular biology programs
GenAL, programme for genomic alignment
Genemaster, used to manipulating gene sequence
Genie, from LBNL, is a gene finder based on generalized hidden Markov models to locate multi-exon genes
GENLANG is a syntactic pattern recognition system that uses tools of computational linguistics to locate genes.
GenomeBrowser is a powerful software tool that simplifies the proccess of analysis, annotation, and manipulation of genetic sequences
Genowiz, is a powerful gene expression analysis program designed to efficiently store, process and visualize gene expression data
GENSEARCH is a user-friendly locus specific software application assisting biologists in the analysis of DNA sequences
GLIMMER , is a program that uses interpolated Markov models to find genes in microbial DNA
GoCore V is a free, open source, "protein sequence alignment and analysis tool
Grail Toolkit. best tools for identifying genes and proteins in the human genome
Genomix GrailEXP6 is created for recognizing splice sites, identifying exon/intron boundaries, and modeling genes.
Iditis - This package provided instant access to protein motifs, substructures and interactions buried in the Brookhaven databank
ISYS, is the National Center for Genome Resources' new product that integrates independent bioinformatic software tools and databases
JalView, it used to view and edit alignment.
JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological pairwise local sequence alignment
LASERGENE is modular, for single users or networks, offering in-depth coverage of sequencing, primer design, sequence alignment, databases and database searching, protein analysis, and restriction map analysis
Look: is a set of informatics tools which allows the researcher to seamlessly access and manage protein sequences, structures
MEGA,a computational analysis of DNA and protein
Mummer, is a system for rapidly aligning entire genome
MacImdad was macromolecular modeling software
MacVector is a set of sequence tools which conduct DNA sequence analysis
MORGAN, is a decision tree program for finding genes in vertebrate DNA.
MPSRCH: is a program which permits rapid searches of DNA and protein sequence data banks using the full Smith-Waterman algorithm
NeoBio is a Java class library of computational biology algorithms
NetPrimer: Performs and prints individual primer and pair analysis using the latest primer design software.
NEWHELIX is a software program for the analysis of oligonucleotide structure
OMIGA sequence analysis tool
Onto-Express automates the process of annotating a set of expressed genes with genomic functions
PAP is a suite of programs to analyze protein structure
PatternHunter is a revolutionary general-purpose homology search tool based on well-recognized, innovative and proprietary technologies
PEAKS is software that identifies proteins and peptides using tandem MS data
PepSeq is a web based training software designed for online computer training of peptide sequencing techniques
Phylip,tool for drawing phylogenetic tree
Plasmid is a new Windows-based vector map drawing and sequence analysis program
PRIMER PREMIER 5: A fully featured, competitively priced primer design program to design specific, sensitive, high yield primers.
PROCHECK , is a program which conducts knowledge-based analysis of protein structures
PROCRUSTES, uses the spliced alignment algorithm, to examine all possible exon assemblies and finds the multi-exon structure with the best fit to related protein.
ProteinSolve is a single-User desktop sofware package for analyzing protein sequence infromation
The Rosetta Resolver System, provides high-capacity data storage, retrieval and analysis of gene expression data.
RGBG Analyzer software is designed for color analysis of digital images
SEQtools 8.2 is a win32 software package for handling and analysis of nucleotide and protein sequences
Sms2, is a sequence manipulation suite for generating, formating and analysing short DNA and protein sequence.
Sectrace, designed to draw pictures ready for publication from secondary structure prediction
SIGNALSCAN, finds homologies in published signal sequences based on the sequence submitted
Solltech DNA fingerprinting and image analysis software
STEM (The Short Time-series Expression Miner) is a Java program for clustering, comparing, and visualizing short time series gene expression data
STRAP is an editor for the multiple sequence alignment of proteins
TESS (Transcription Element Search Software), is a system for locating and displaying transcription factor binding sites in DNA sequences.
TurboBLAST is an accelerated, parallel implementation of BLAST, a sequence comparison tool that provides critical insight into the structure and function of genes and proteins
UniPro DPview is a powerful tool for analyzing genetic sequences
Vector gives researchers the power to analyze proprietary sequences in the context of human genome project data.
VIBE (Visual Integrated Bioinformatics Environment). a next generation visualization and genomics discovery too
Visual Cloning 2000 is an advanced new vector map drawing and sequence analysis program
The Wisconsin Package a sequence analysis contains over 100 interrelated software programs. It enables scientists to analyze DNA and protein sequences by editing, mapping, comparing, and aligning them.