| FASTA to multi-FASTA converter
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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: FASTA 2 multiFASTA
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| ABI to FASTA free converter
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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. |
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Web Site: DNA Baser Contig Assembler
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| ALIGN
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Internet Browser Windows |
| Aligns two sequences. |
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Web Site: Genestream (IGH)
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| ALP3/ALN3 1.0
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MS-DOS |
| Alignment of three protein or DNA sequences using an efficient traceback procedure. |
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Download (100 kb, 17-Nov-1989) |
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| AMAS
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Internet Browser Unix |
| Analyse multiply aligned protein sequences to find likely functional residues. |
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Web Site: EBI
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| AMPS
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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. |
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Web Site: G. Barton, University of Oxford
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| AiO
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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.......... |
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Web Site: AiO - All in One - AiO
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| Align
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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). |
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Download (505 kb, 04-Jun-1993) |
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| Align: Compendium of Protein Sequence Alignments
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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. |
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Web Site: Biomolecular Structure and Modelling Unit, University College London
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| Aligner
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Internet Browser |
| With this tool you can align easily your multiple sequences DNA or protein, based on a Clustalw engine. |
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Web Site: JustBio.com
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| AlleleID 4
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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. |
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Web Site: PREMIER Biosoft
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| AlleleID version 6
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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. |
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Web Site: Premier Biosoft
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| AmiraMol
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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: |
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Web Site: AmiraMol
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| Antheprot 2.9
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MS-DOS Unix Windows |
| This is a protein sequence analysis package. |
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Web Site: Institut de Biologie et Chimie des Proteines
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| ApE
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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. |
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Web Site: ApE- A plasmid Editor
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| BLAST 2.0
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Internet Browser MS-DOS |
| A tool used to identify any potential homologies of a given DNA or protein sequence with those stored in GenBank. |
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Web Site: NCBI
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| BOXSHADE 2.6
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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. |
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Download (360 kb, 27-May-1994) |
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| BOXSHADE 3.0
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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. |
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Download (91 kb, 29-Mar-1996) |
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| BioEdit
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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. |
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Web Site: Department o Microbiology, North Carolina State Unversity
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| BioMedCAChe
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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. |
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Web Site: BioMedCAChe - Software for bio and medicinal Chemists
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| Bork's alignment tools
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Internet Browser |
| Various tools to enhance the results of multiple alignments (including consensus building). |
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Web Site: EMBL
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| CINEMA
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Internet Browser |
| CINEMA is a Colour INteractive Editor for Multiple Alignments. The program allows visualisation and manipulation of both protein and DNA sequences. |
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Web Site: University College London
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| CLC Bioinformatics Cell
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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. |
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Web Site: CLC Bioinformatics Cell
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| CLC Combined Workbench
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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 |
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Web Site: CLC bio
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| CLC Free Workbench 1.0
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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 |
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Web Site: CLC bio
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