Sequence

From Bioinformatics.Org Wiki

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
• UGENE - a free and open source DNA and protein sequence analysis tool. The goal of the project is to integrate most of the available command line utilities into a single graphical package.