| FASTA Merger - freeware
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Windows |
| This tool will look for all FASTA files in the specified folder and will merge their content in a single file. |
 Web Site: DNA Baser
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| 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! |
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Web Site: FASTA 2 multiFASTA
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| Multi-FASTA to FASTA converter
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Mac Windows |
| This FREEWARE program will split a multi-FASTA file in multiple standard FASTA files. |
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Web Site: multiFASTA spliter
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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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| AGM Build
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Linux Windows |
| A molecular builder and conformational editor. AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. Features: * Geometry editing * Lattice building * Building of chain molecules * Chains with predetermined conformations * Charges and atom types according to selected Force Field |
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Web Site: Agile Molecule
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| Abalone
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Windows |
| a program for biomolecular modeling. General Features: Molecular Dynamics, optimization, implicit and explicit water. |
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Web Site: Agile Molecule
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| Advanced planning and production scheduling software for biotechnology companies
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Windows |
| We develop and market advanced planning and production scheduling software for biotechnology companies around the world. |
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Web Site: Taylor Scheduling Software
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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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| 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 5
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| AlleleID designs real time PCR and microarray probes and primers for identifying strains and sequences from an alignment and for amplifying and detecting patterns across sequences. AlleleID has a built-in ClustalW alignment module which aligns the nucleotide sequences. You can choose to amplify and detect sequence specific or conserved regions from the mix. AlleleID supports TaqMan, molecular beacons, Fret, TaqMan MGB and Microarray probes. A distinguishing feature of AlleleID is the ability to design real time PCR primers and probes to spot and amplify exons/introns |
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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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| 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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| Array Designer 4
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Linux Windows |
| Array Designer designs highly efficient, specific oligos for SNP genotyping, and expression microarrays. You can start with a list of sequences or the whole genome sequence in standard format to study entire organisms effortlessly. Using a sophisticated algorithm, the program automatically interprets BLAST results and designs highly specific oligos. The oligos and templates can then be BLAST searched against private local databases or all genomic public databases available at NCBI, including the redundant nr database to verify the specificity of the design. With Array Designer, you can even design tiling arrays to spot every base of a long genomic sequence, avoiding repetitive regions. Designing arrays to characterize regulatory elements, or to study epigenetic modifications, methylation patterns and protein binding sites has never been so easy. |
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Web Site: www.premierbiosoft.com
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| Ascalaph
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Linux Windows |
| Molecular Modelling Suite. * Molecular Design * Molecular mechanics simulations * Quantum calculations * Force Field development * GPU accelerated Molecular Dynamics |
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Web Site: Agile Molecule
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| Ascalaph Quantum
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Windows |
| 3D graphic interface for the Quantum Mechanics program PC GAMESS. Ascalaph Quantum provides the generation and editing of molecular models. |
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Web Site: Agile Molecule
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| Beacon Designer
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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 |
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Web Site: PREMER Biosoft International
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| Beacon Designer 4
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Mac Windows |
| Beacon Designer is a tool for designing primers and probes for real time detection of PCR products and for multiplex and allele discrimination assays. It designs SYBR Green primers, TaqMan® probes, FRET probes and molecular beacons for robust amplification and fluorescence in real time QPCR. It also evaluates pre-designed/published beacons and primers. Beacon Designer displays secondary structures in a graphical format for easy interpretation, uses statistical optimization techniques to output the best rated primer/probe pair and generates a list of alternate probes to meet specific research needs and allows complete control over design parameters. |
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Web Site: www.premierbiosoft.com
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| Beacon Designer Free Edition
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Internet Browser |
| Beacon Designer Free Edition is a free web based oligo properties calculator for analysing SYBR Green Primers and TaqMan Probes for possible secoondary structures such and for accurately calculating Primer and Probe Tm. Beacon Designer free edition also displays sequence details such as sequence length, runs, repeats, reverse, reverse complement and GC%. |
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Web Site: Premier Biosoft
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| Becoming a Successful Scientist
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Internet Browser |
| Provides information and links of interest on succeeding in scientific research. |
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Web Site: Becoming a Successful Scientist
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| BibioSphere PathwayEdition
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Internet Browser Linux Mac Unix Windows |
| BiblioSpherePE allows for dynamic data-driven network/pathway construction and analysis based on literature, the Genomatix Knowledge Base, and promoter DNA sequence analysis. It is an important component of the micro array data analysis pipeline offered by Genomatix. |
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Web Site: Genomatix
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| BioMapper
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Internet Browser Windows |
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Web Site: BIOGIS Biodiversity, Geo and Metadata Management Solutions
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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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| BioOffice
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Internet Browser Windows |
| BioOffice from BIOGIS Consulting is a tool for input, mapping, spatial analysis and exchange of biological distribution data and collections. This application for professional biodiversity data management is used at many natural history museums and universities in Europe and also in international projects. |
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Web Site: BioOffice Biodiversity Data Management Solutions
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| BioReagent LIMS
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| BioRoot Bioinformatics is a non-profit organization dedicated to fostering communication, collaboration, and increased productivity in the biological sciences through information exchange. We provide a free centralized database service to collect, store, and disseminate information about commonly used molecular biology reagents: oligonucleotides, plasmids, and strains. Use of this bio-reagent LIMS will cut costs, save time, and accelerate research benefiting the bench scientist, the PI, and the patient. |
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Web Site: BioRoot Bioinformatics
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| Biochemistry, Molecular Biology, and Cell Biology Protocols
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| Life sciences methods and protocols focusing on biochemistry, molecular biology, and cell biology experiments. |
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Web Site: Biochemistry, Molecular Biology, and Cell Biology Protocols
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