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FASTA to multi-FASTA converter Mac  Windows
This freeware tool will look for all FASTA files in the specified folder and will merge their content in a single file, generating a standard or custom Multi-FASTA file. FREEWARE!
Web Site Home Web Site: FASTA 2 multiFASTA

Multi-FASTA to FASTA converter Mac  Windows
This FREEWARE program will split a multi-FASTA file in multiple standard FASTA files.
Web Site Home Web Site: multiFASTA spliter

2D Hunt Internet Browser
2-D Electrophoresis Finder provides an interface for searching 2D electrophoresis-related pages on the web, by keyword.
Web Site Home Web Site: Expasy

ABI to FASTA free converter Windows
This free tool will batch convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogram files and press the CONVERT button. With this automatic converter you can convert hundreds or thousands of ABI chromatogram files in seconds. All with A SINGLE PUSH OF A BUTTON! ---------- No installation process is required.
Web Site Home Web Site: DNA Baser Contig Assembler

AiO Windows
Software package combining DNA/protein programs with oligonucleotide Data Base management. It is written multi-user and multi-group. However, it can be run on a single PC for single user. Features: DNA-editor, DNA with restriction enzymes, DNA with oligos, PCR tables, plasmid maps, linear maps, dotplot, alignments, ORF finding, translate, backtranslate, flow (virtual cloning), editors for data banks (oligos, structural DNA etc), online oligo ordering..........
Web Site Home Web Site: AiO - All in One - AiO

Aligner Internet Browser
With this tool you can align easily your multiple sequences DNA or protein, based on a Clustalw engine.
Web Site Home Web Site: JustBio.com

AlleleID 4 Mac  Windows
AlleleID supports real time PCR primer design, design of TaqMan, SYBR Green primer design, TaqMan MGB probe design and design of microarrays for detecting gene splicing and alternative splicing. AlleleID can be used to design cross species assays, assays for bacterial identification, species identification and strain detection. You can align the nucleotide sequences to locate differences in DNA and to find unique or conserved regions and then design oligos to amplify and detect either species or strains of interest from the mix. AlleleID also supports assays for selectively amplifying cDNA from gDNA.
Web Site Home Web Site: PREMIER Biosoft

AlleleID version 6 Mac  Windows
AlleleID the comprehensive primer design tool can now design mutation specific/mRNA specific or DNA specific MLPA probes that are compatible with Pamchip array.
Web Site Home Web Site: Premier Biosoft

ApE Linux  Mac  Unix  Windows
ApE is designed to be an all-in-one molecular biology workbench. It can read strider, EMBL, genbank, Fasta sequence file formats. In addition it can read and display ABI trace files. It can query and download from the NCBI EMBL database and can blast sequences directly at the NCBI BLAST server. Sequence features can be added individually or automatically from pre-defined feature definition libraries. It can draw graphic (liear or circular) and text-based restriction maps that include annotated features of the sequence. It contains a restriction enzyme choser that can perform boolean queries for enzymes that match cut frequency and enzyme property parameters. It can show virtual agarose gels. It can align two sequences or a sequence and an ABI trace file. It can search selected sequence for potential PCR primers matching given parameters. All analysis functions are hyperlinked back to the original sequence. Other features of the program are listed on the website.
Web Site Home Web Site: ApE- A plasmid Editor

Artemis Linux  Mac  Unix  Windows
Artemis is a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, reads EMBL-format sequences and feature tables, and can work on sequences of any size from a few kb to entire genomes of 5 Mb or more. Written in Java.
Web Site Home Web Site: Sanger Center

BLAST Unix  Windows
Source code for the Basic Local Alignment Search Tool (BLAST) family of sequence database comparison programs, along with some support utilities and (new) awk scripts. Source code from the programs NCBI, GISH and DFA are required to compile and link the BLAST programs.
Download  (330 kb, 15-Sep-1991)

BLAST 2.0 Internet Browser  MS-DOS
A tool used to identify any potential homologies of a given DNA or protein sequence with those stored in GenBank.
Web Site Home Web Site: NCBI

BLASTView Internet Browser
Demonstration of bioWidgets toolkit for processing BLAST search results.
Web Site Home Web Site: CBIL, University of Pennsylvania

Beacon Designer Mac  Windows
Beacon Designer is a comprehensive real time PCR primer and probe design tool that is supported on Win amd Mac OS. Beacon Designer designs optimal SYBR® Green primers, TaqMan® probes, LNA spiked TaqMan® probes, molecular beacon for both standard and NASBA® assays, and FRET probes for real time quantitative PCR assays. Highly specific primers are designed by avoiding cross homologies found by automatically interpreting BLAST search results. Primer efficiency is enhanced by avoiding template secondary structures identified by connecting to the Mfold server. Beacon Designer can be used to evaluate predesigned assays and designing compatible oligos to extend the designs. It can design molecular beacons and TaqMan® probes for single tube multiplex experiments. Version 6 of Beacon Designer helps researchers design MethyLight assays using TaqMan probes for detecting DNA methylation and predicting CpG islands using real time PCR
Web Site Home Web Site: PREMER Biosoft International

Bic Internet Browser  Unix
Ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator.
Web Site Home Web Site: EBI

BioEdit Windows
BioEdit is a full integrated sequence/alignment editor. Performs translations, phylogenetic analysis, clustalw alignments, ABI trace analysis, RNA comparitive analysis and BLAST searches. Freeware.
Web Site Home Web Site: Department o Microbiology, North Carolina State Unversity

BioNumerics Windows
One universal bioinformatics solution to store and analyze all your biological data. Powerful databasing, integrated networking and a wide range of analysis, visualization and decision-making tools, including data mining, querying, clustering, identification, statistics, and much more. With applications for bacteriology, virology and mycology including features for surveillance networks for bacterial (Salmonella, E. coli & Shigella, Campylobacter spp., Listeria monocytogenes, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis, etc.) and viral pathogens (norovirus).
Web Site Home Web Site: Applied Maths

Blast Client 1.8 Mac
Interface for the BLAST database server.
Download  (296 kb, 15-Sep-1991)

CBLAST 1.1 Unix
BLAST output parser. Requires C compiler (source code only).
Download  (210 kb, 18-Apr-1997)

CELL Suite Windows
Incellico's Cell Suite being offered as a modular portfolio of research and discovery tools that will individually, and as a whole, respond to the specific challenges faced by life sciences researchers across the spectrum of biotechnology and bioinformatics problem solving. CELL acts as a librarian of public and private databases, automatically cross-referencing entities like genes and proteins that appear in those databases, and building a searchable, ontology-based network of cross-references that reveals the relationships between entities of interest to a user.
Web Site Home Web Site: Incellico

CLC Bioinformatics Cell Linux  Mac  Windows
CLC Bioinformatics Cell is a High Performance Computing product, accelerating Smith Waterman based BLAST-searches up to 400 times and Clustal W alignments up to 20 times. It can be run command line with the same parameters as NCBI BLAST, or through the graphical user interface of CLC Gene Workbench, CLC Protein Workbench, or CLC Combined Workbench.
Web Site Home Web Site: CLC Bioinformatics Cell

CLC Combined Workbench Linux  Mac  Windows
CLC Combined Workbench 1.0 aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench. All analyses are fully integrated in one single, user-friendly, and intuitive software application. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Protein family analysis (PFAM) - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, SwissProt, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Free Workbench 1.0 Linux  Mac  Windows
CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options. Some bioinformatics features are: - GenBank searching and viewing (linear and circular views) - Multiple alignment of DNA, RNA and proteins (2 alignment algorithms) - Open reading frame determination - Translation from DNA to proteins (all genetic translation tables) - Reports with residue composition, molecular weight and iso electric point (for proteins) - Neighbor-joining and UPGMA phylogenies - Restriction site analysis and viewing - Other reporting facilities - Import/export to a number of data formats - Launch of external files - Detailed History Log
Web Site Home Web Site: CLC bio

CLC Gene Workbench Linux  Mac  Windows
CLC Gene Workbench 1.0 provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Searches on GenBank and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Protein Workbench Linux  Mac  Windows
CLC Protein Workbench 1.5 provides a wide range of advanced protein sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Advanced and integrated 3D molecular viewer - 2 types of alignments - Phylogenetics - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Protein family analysis (PFAM) - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, Swiss-Prot, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

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