| DCSE 1.18
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MS-DOS |
| DCSE (Dedicated Comparative Sequence Editor) provides a user-friendly, menu-driven environment to make and maintain sequence alignments. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment. |
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Download (618 kb, 01-Jan-1995) |
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| DCSE Manual
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Unix |
| Instructions for DSCE. |
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Download (82 kb, 04-Jan-1995) |
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| DIALIGN
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Linux Unix |
| This is a multiple sequence alignment program that compares whole segments rather than single residues. |
 Web Site: AG BIODV
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| DIALIGN 2
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Internet Browser |
| Alignment of multiple sequences using this novel algorithm based on segment to segment comparison. |
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Web Site: University of Bielefeld
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| DNA Baser - an affordable alternative to the really expensive software on the market
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Mac Windows |
| DNA Baser has been designed as a tool for fast assembly of DNA sequences. We had in mind a fast assembly engine and implementation of a number of features that greatly reduce the required user input. These features (see the Features page) have been successfully implemented, so that the current version of DNA Baser can assemble 4 trace files with about 800 nucleotides each within 2 seconds on an average system configuration. End trimming of the original trace files, suggestions for correction of ambiguous bases based on quality values, automatic removal of cloning vector sequences from the final contig are only some examples of fully functional features that makes the assembly of DNA sequences much easier and less time-consuming. Some of the alignment core features are: * Very fast assembly algorithm: the assembly of four SCF files with 800 nucleotides each takes less than 3 seconds on an average computer (AMD/INTEL 1.2 GHz) * It will automatically clean (trim) the ends of o chromatogram if the Quality Values (QV) is very poor. The resolution of the trimming engine can be fully adjusted by the user; this operation saves significant time, as manual ‘cleaning’ of the trace sequences is not needed any more. * The original trace files and the generated contig are synchronized and displayed as such, making the correction of ambiguous bases much easier * Using the QV, DNA Baser makes suggestions for correction of the ambiguous bases; the rate of correct suggestions recorded during testing was more than 95%. This means that the user must only confirm the software’s suggestions, which again decreases the overall processing time * Reverse-complement: reverse sequences are automatically turned during assembly * Automatic cut of vector/primer sequence. Create your own primer database by adding your primers. Using this database, DNA Baser will remove the primer from the final contig * Viewing of trace files (format ABI and SCF) Special features * BEST price on the market and significant discount when several licenses are ordered. Please see the Prices page for more details * Intelligent, ergonomic, easy to use interface. Just drag and drop your files, then press the |
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Web Site: DNA Baser - DNA assembly tool
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| DNA for Windows
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Windows |
| A compact DNA sequence analysis program, with features including sequence editing, translation, restiction site location, contig assembly, codon usage and chromatogram (ABI, SCF) file viewing, editing, printing and aligning. Registered version is now fully Windows XP compatible. |
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Web Site: DNA for Windows
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| DNATools
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Windows |
| DNATools has now been discontinued and replaced with SEQtools. SEQtools is a program for handling and analysis of nucleotide and protein sequences. In addition to many trivial functions, SEQtools includes advanced facilities for automated blast searching, sequence retrieval and design and layout of microarrays. |
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Web Site: SEQtools
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| DiAlign
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Internet Browser Linux Unix |
| True multiple sequence alignment, not Needleman-Wunsch based. * No gap penalties (gaps are not introduced by the original alignment). * Alignment of whole segments and not of individual nucleotides or amino acids. * True multiple alignment, therefore independent of sequence order. * True multiple alignment of 200 sequences can be carried out on a workstation. |
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Web Site: Genomatix
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| Dtask 1.1s
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Unix |
| Dtask is a program package for running unix workstations in parallel when comparing a protein- or DNA/RNA-sequence (using Smith-Waterman search algorithm) against a library of such sequences. |
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Download (306 kb, 26-Apr-1993) |
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| ESEE 1.09d
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MS-DOS |
| The EyeBall Sequence Editor (ESEE) is a multi-sequence editing program specifically developed for the entry, manipulation and presentation of nucleic acid and amino acid sequences. |
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Download (130 kb, 25-Jun-1990) |
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| EdIt
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Linux Unix |
| Automatic editing/finishing of shotgun DNA projects. Key features of EdIt include: a dedicated process to generate edit hypotheses that can handlecomplex multi fault editing problems. The artificial neural network approach used for decision makingprovides the possibility to cope with new or different sequencing technology by training new networkswithout detoriorating the quality of the results. Hidden data (data with low quality) is used for makingfault regions double stranded if possible and necessary. EdIt is independent from specific finishingtools (caf input and output ensures portabilitly to current finishing tools). Different parameters areavailable to control the boldness of the editor. Edit operations are marked by tags. |
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Web Site: The MIRA-EdIt Project
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| ElDorado/Gene2Promoter
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Internet Browser Linux Mac Unix Windows |
| More than 100 gigabytes of condensed, filtered, quality checked and ranked information on morte than 10 genomes. A condensation of publicly available data from a variety of resources plus Genomatix proprietary annotation, including promoters, transcription factor binding sites, promoter modules, scaffold/matrix attachment regions, single nucleotide polymorphisms, and much more. |
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Web Site: Genomatix
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| Exploratory Analysis of Multiple Sequence Alignments
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MS-DOS |
| Exploratory Analysis of Multiple Sequence Alignments. The purpose of this program is to aid data exploration of such multiple sequence alignment programs. |
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Download (120 kb, 19-Feb-1993) |
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| Expression
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Windows |
| Expression is a revolutionary new application for DNA and protein sequence analysis. Utilising a novel interface, Expression makes complex computational analyses of sequence information incredibly simple. Expression uses the very latest computing technology to set new standards in the way sequences are analysed. Features include: Sequence Annotation,Graphical Sequence Map, Degenerate DNA and Amino Acid Sequence Support, Restriction Analysis, Primer Design and Analysis, ORF Prediction, Pattern Finding, Reverse Translation, GenBank Searching, Pattern and Motif Identification, Multiple Sequence Alignment, and Protein Structure Prediction. |
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Web Site: Genamics
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| FASTA-BLAST Scan
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Windows |
| FASTA/BLAST Scan parses your FASTA or BLAST results and allows you to save sequences of real interest for you in a Pearson format multi-sequence file. This file is compatible with the CLUSTALW program. |
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Web Site: Olivier Friard
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| Fast chromatogram viewer
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Windows |
| This freeware tool will list all chromatogram files (SCF, ABI, AB1, AB) in the current folder. You can view the chromatogram by simply clicking a file. Install process: You do not need to install it. Just download the program and double click to run it. It does not need additional software, updates, DLLs or Java to run it. To uninstall it just delete the program. |
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Web Site: Fast chromatogram viewer
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| Filter
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Unix |
| Set of programs for suboptimal alignments and recognitionof reliably aligned regions in protein sequence comparisons and to multiply align and find conserved motifs from a set of sequences. |
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Download (80 kb, 16-Dec-1992) |
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| GDE
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Unix |
| Expandable set of programs for multiple sequence alignment and analysis (binaries). For the Sun series of workstations. |
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Download (271 kb, 01-Jul-1991) |
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| GDE Documentation
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Unix |
| Expandable set of programs for multiple sequence alignment and analysis (documentation - Postscript). |
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Download (94 kb, 01-Jul-1991) |
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| GDE Source Code
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Unix |
| Expandable set of programs for multiple sequence alignment and analysis (source code). For the Sun series of workstations. |
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Download (280 kb, 01-Jul-1991) |
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| GENtle
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Windows |
| GENtle is a program for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, specialized calculators, PCR, gel image display, virtual gel simulation, and more. |
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| GenAl 2.1
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Unix |
| GenAl is a program for genomic alignment, i.e. alignment of DNA sequences with coding regions. |
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Download (55 kb, 07-Mar-1994) |
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| Genchek
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Linux Mac Unix Windows |
Genchek is a comprehensive, multi-platform, sequence analysis software package. It facilitates analysis of Expressed Sequence Tags (ESTs), Complete Genome, and SNP (Single Nucleotide Polymorphism) data. Genchek is a research information and experiment management tool that integrates public and proprietary data through a discovery workspace that provides contextual access to sequence analysis tools, content and services. Genchek has an integral database system that can be used to access, store, organize and retrieve DNA, protein and vector sequences in an intuitive environment that offers editing, management and annotation of sequences. |
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Web Site: Ocimum Biosolutions - BioIT - Bioinformatics - Genchek?
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| GeneCoder
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Linux Mac Unix Windows |
| GeneCoder is a freely available, multi-platform utility to analyze both DNA and protein sequences. Compatible with a large array of file formats, GeneCoder contains a variety tools, including tools to analyze Restriction Sites, create Restriction Site Maps, perform sequence alignments, analyze oligonucleotides, remotely access NCBI, and much, much more. A more detailed description of GeneCoder capabilities can be found at the GeneCoder Software webpage. |
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Web Site: Algosome
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| GeneDoc
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Windows |
| GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support. |
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Web Site: Ketchup
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