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Category bioinformatik.de / Software / Unix / Sequence Analysis /

Acedb is a genome database system. The program is used both for managing data within genome projects, and for making genomic data available to the wider scientific community.
http://www.sanger.ac.uk/Software/Acedb/

Alfresco - The program will compare multiple sequences from putitatively homologous regions in different species.
http://www.sanger.ac.uk/Software/Alfresco/

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.
http://www.sanger.ac.uk/Software/Artemis/index.shtml

Belvu is an X-windows viewer for multiple sequence alignments.
http://www.cgr.ki.se/cgr/groups/sonnhammer/Belvu.html

Blixem, which stands for "BLast matches In an X-windows Embedded Multiple alignment", is an interactive browser of pairwise Blast matches that have been stacked up in a "master-slave" multiple alignment.
http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html

CHROMA: consensus-based colouring of multiple alignments for publication.
http://www.lg.ndirect.co.uk/chroma/

CLC Gene Workbench is a software suite with a range of advanced and integrated DNA sequence analysis tools - among others, assembly of DNA sequence data, advanced primer design, and molecular cloning. Available for Windows, Mac OS X, and Linux.
http://www.clcbio.com/index.php?id=27

CLC Protein Workbench is a software suite with a range of advanced and integrated protein sequence analysis tools - among others, secondary structure and signal peptide prediction, and hydrophobicity analyses. Available for Windows, Mac OS X, and Linux.
http://www.clcbio.com/index.php?id=93

Correspondence Analysis of Codon Usage
http://www.molbiol.ox.ac.uk/cu/

Darwin stands for Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences.
http://cbrg.inf.ethz.ch/Darwin/index.html

Delila - Software for Information Analysis of Protein and Nucleic-acid Sequences, including Sequence Logos and Sequence Walkers.
http://www-lecb.ncifcrf.gov/~toms/delila.html

Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences.
http://bibiserv.TechFak.Uni-Bielefeld.DE/dca/

Dotter is a graphical dotplot program for detailed comparison of two sequences.
http://www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html

ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences.
http://prodes.toulouse.inra.fr/ESPript/ESPript/

ESTatePage - Expressed Sequence Tag Analysis Tools Etc.
http://fe.hgmp.mrc.ac.uk/gslater/wwx/webwebx.cgi?ViewPage=ESTatePage

FAKtory: A software environment for DNA Sequencing Projects.
http://www.cs.arizona.edu/faktory/

GCUA: General Codon Usage Analysis. This program is useful for carrying out analysis of variation in codon usage within a collection of genes such as might be found in a complete genome. Some of the most popular multivariate analysis methods are implemen
http://bioinf.nuim.ie/gcua/

Genetics Computer Group (GCG)- Software for the Analysis of Genes and Proteins
http://www.accelrys.com/about/gcg.html

GenomeInspector - Software for the analysis of spatial correlations of elements on DNA sequences.
http://www.gsf.de/biodv/genomeinspector.html

Geospiza - Software for Molecular Biology
http://www.geospiza.com/

HMMER 2.1.1 - Profile hidden Markov models for biological sequence analysis.
http://hmmer.wustl.edu/

Jalview - a java multiple alignment editor.
http://www2.ebi.ac.uk/~michele/jalview/contents.html

MatInspector - a tool for detection of transcription factor binding sites.
http://www.gsf.de/biodv/matinspector.html

MatrixPlot can be used to generate mutual information plots of sequence alignments, distance matrices of sequence with known 3D coordinates, and plots of user provided matrix files.
http://www.cbs.dtu.dk/services/MatrixPlot/

mira - a DNA sequence data assembler
http://www.chevreux.org/uploads/media/mira.html

ModelGenerator an ModelInspector - Methods for definition and recognition of complex organizational patterns in DNA sequences.
http://www.gsf.de/biodv/modelinspector.html

NHGRI WebBLAST is a suite of software tools to aid in viewing and organizing genetic sequencing data.
http://research.nhgri.nih.gov/software/webblast/

Parallel CLUSTAL W/CLUSTAL X and HT_Clustal for IRIX.
http://www.sgi.com/chembio/resources/clustalw/parallel_clustalw.html

Phrap and Phred for Windows, MacOS, Linux, and Unix - Fast sequence assembly and better base calling.
http://www.phrap.com/index.htm

PROCRUSTES: Gene Recognition via Spliced Alignment
http://www-hto.usc.edu/software/procrustes/index.html

SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE).
http://pbil.univ-lyon1.fr/software/seaview.html

SeqPup - a biosequence editor and analysis program.It includes links to network services and external analysis programs.
http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/seqpup-doc.html

SIMPLE34 - The aim of the program is to estimate the level of local sequence repetition in nucleotide sequences.
http://life.anu.edu.au/molecular/software/simple.html

Staden Package WWW site
http://www.mrc-lmb.cam.ac.uk/pubseq/

TeXshade is an alignment shading LaTeX macro package for processing multiple sequence alignments. It provides special shading modes featuring functional aspects, e.g. charge, and a plenitude of commands for handling shading colors, text styles and labels.
http://homepages.uni-tuebingen.de/beitz/tse.html

TeXtopo - A LaTeX package for shaded membrane protein topology plots.
http://homepages.uni-tuebingen.de/beitz/tte.html