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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

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

ALIGN Internet Browser  Windows
Aligns two sequences.
Web Site Home Web Site: Genestream (IGH)

ALP3/ALN3 1.0 MS-DOS
Alignment of three protein or DNA sequences using an efficient traceback procedure.
Download  (100 kb, 17-Nov-1989)

AMAS Internet Browser  Unix
Analyse multiply aligned protein sequences to find likely functional residues.
Web Site Home Web Site: EBI

AMPS Unix
A suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures, and also implements flexible pattern matching and database scanning options.
Web Site Home Web Site: G. Barton, University of Oxford

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

Align Mac
This archive contains a series of programs for use in PROTEIN sequence alignment and phylogenetic tree construction. The logic of the method is described in the article "Progressive Sequence Alignment As A Prerequisite to Correct Phylogenetic Trees" by D. F. Feng and R. F. Doolittle in J. Mol. Evol. 25:351 (1987).
Download  (505 kb, 04-Jun-1993)

Align: Compendium of Protein Sequence Alignments Internet Browser
ALIGN is a compendium of sequence alignments: it is a companion resource to PRINTS. For each fingerprint, there is a corresponding alignment in NBRF format, the root name of which is the relevant PRINTS code. The database codes used in the alignments reflect the primary source from which they came: the codes may change between database releases, so alignments derived from early versions of OWL will include original rather than current codes.
Web Site Home Web Site: Biomolecular Structure and Modelling Unit, University College London

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

AmiraMol Linux  Unix  Windows
Together with Amira 2.3, an object-oriented interactive system for 3D data visualization, the new extension AmiraMol has been released. AmiraMol adds advanced tools for the visualization of Molecules. It combines Amira's strong capabilities for 3D data visualization like hardware accelerated volume rendering with specific tools for molecular visualization and data analysis. AmiraMol is available for Windows, Linux, IRIX, HP-UX, and SunOS. To get more information or to download a free trial version of Amira please visit our website:
Web Site Home Web Site: AmiraMol

Antheprot 2.9 MS-DOS  Unix  Windows
This is a protein sequence analysis package.
Web Site Home Web Site: Institut de Biologie et Chimie des Proteines

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

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

BOXSHADE 2.6 Unix
BOXSHADE is a program for creating good looking printouts from multiple-aligned protein or DNA sequences. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor.
Download  (360 kb, 27-May-1994)

BOXSHADE 3.0 MS-DOS  Unix  VMS
BOXSHADE is a program for creating good looking printouts from multiple-aligned protein or DNA sequences. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor. This archive file contains a DOS executable and universal PASCAL source code together with appropriate makefiles or scripts for building the program for other systems.
Download  (91 kb, 29-Mar-1996)

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

BioMedCAChe Linux  Mac  Unix  Windows
BioMedCAChe is a new computer-aided chemistry software package designed specifically for bio- and medicinal chemists. It provides powerful software tools to accelerate the drug discovery process. BioMedCAChe enables to analyze protein sequences and optimize their 3D structures, build protein structures by homology, dock ligands, and model enzyme reactions using whole enzymes.
Web Site Home Web Site: BioMedCAChe - Software for bio and medicinal Chemists

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

Bork's alignment tools Internet Browser
Various tools to enhance the results of multiple alignments (including consensus building).
Web Site Home Web Site: EMBL

CINEMA Internet Browser
CINEMA is a Colour INteractive Editor for Multiple Alignments. The program allows visualisation and manipulation of both protein and DNA sequences.
Web Site Home Web Site: University College London

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

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