Sequences

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Software

  • ARB - Microbiologist's sequence database tool
  • Artemis - 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.
  • autoseq - a small package of base calling software for ABI automated DNA sequencers
  • Biogrep - A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
  • BioJava - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
  • Biopython - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
  • BioWish - Biowish is a C-extension for the Tcl/Tk scripting language
  • BLAST - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
  • Chimera - Excellent molecular graphics package with support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven analysis, multiple sequence alignment analysis, multiple model analysis, dockin
  • clustalw - The famous ClustalW multiple alignment program
  • clustalx - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
  • consed - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
  • DBWatcher - DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.
  • DNA-GUI - DNA Graphical User Interface
  • EMBOSS - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
  • Friend - Friend, an Integrated Front-end Application for Bioinformatics
  • gBioSeq - Biological sequence (ADN, protein) editor for GTK/Linux
  • Genpak - a set of small utilities written in ANSI C to manipulate DNA sequences in a Unix fashion, fit for combining within shell and cgi scripts
  • JAligner - JAligner is a Java implementation of biological sequence alignment algorithms.
  • libGenome - A cross platform C++ development library to manipulate DNA and protein sequences. It can read and write sequence and annotation data in several file formats.
  • ModView - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
  • MPSRCH - MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
  • Musca - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
  • MUSCLE - Multiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
  • NCRNASCAN - a structural RNA genefinder
  • PatScan - PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
  • PhyloDraw - PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
  • PKNOTS - RNA pseudoknot prediction
  • Pratt - a pattern discovery tool
  • readseq - Reads and writes nucleic/protein sequences in various format
  • SAM equence Alignment and Modeling Syste - a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
  • SEALS - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
  • seaview - SeaView is a graphical multiple sequence alignment editor
  • SeqPup - SeqPup biological sequence editor and analysis program
  • ShadyBox. - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
  • sp2fasta - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
  • Toucan - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
  • tRNAscan-SE - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
  • WU-Blast - Washington U. BLAST
Retrieved from "http://wiki.bioinformatics.org/Sequences"
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