Software

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===A===
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== Popular software for bioinformatics ==
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* [[Abacus]] - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
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Everyday bioinformatics is done with sequence search programs like [[BLAST]], sequence analysis programs, like the [[EMBOSS]] and [[Staden Package|Staden]] packages, structure prediction programs like [[THREADER]] or [[PHD]] or molecular imaging/modelling programs like [[RasMol]] and [[WHAT IF]].
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* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project
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* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.
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* [[Amplicon]] - Program for designing group-specific PCR primer sets
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* [[Angler]] - A Browser of C.elegans Embryo Development In Time and Space
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* [[ARB]] - Microbiologist's sequence database tool
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* [[Arka]] - graphical interface for the programs from the GP (Genpak) package
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* [[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.
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* [[ATV]] - a phylogenetic tree display tool
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* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
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===B===
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More:
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* [[NetSurfP]] - Protein Surface Accessibility and Secondary Structure Predictions
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* [[NetTurnP]] - Prediction of Beta-turn regions in protein sequences
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* [[MODELLER]] - Used for homology or comparative modeling of protein three-dimensional structures
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* [http://autodock.scripps.edu/ AutoDock] - Suite of Automated Docking Tools
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* [http://www.gromacs.org/ Gromacs] - A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids
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* [[Babel]] - a program designed to interconvert a number of file formats currently used in molecular modeling
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== Popular Linux OS distributions for bioinformatics ==
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* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
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* [[BioJava]] - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
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* [[Biolisp]] - BioLisp.org is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences.
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* [[BioMail]] - automate searching for recent scientific papers in the [[PubMed]] Medline database
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* [[Bioperl]] -  open source Perl tools for bioinformatics, genomics and life science research
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* [[Biopython]] - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
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* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
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* [[Blast]] - BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
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* [[Blixem]] - 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.
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* [[BRAGI]] - BRAGI is a interactive protein modelling and display program. It was developed for the special purpose to modell unknown proteins from the structure of  a known one
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===C===
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* [http://www.gentoo.org/ Gentoo Linux] ([http://packages.gentoo.org/category/sci-biology?full_cat List of bioinformatics packages])
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* [http://bioknoppix.hpcf.upr.edu/ Bioknoppix]
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* [http://biopuppy.org BioPuppy] - A Minimal Linux OS for Bioinformatics
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* [http://nebc.nox.ac.uk/tools/bio-linux/bio-linux-5.0 BioLinux]
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* [http://opendiscovery.org.in Open Discovery] - An integrative bioinformatics linux distro with high performance computing capability
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* [http://www.bioslax.com/ Bioslax]
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* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
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Generic yet popular distributions:
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* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
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* [http://www.ubuntu.com/ Ubuntu]
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* [[Chimera]] - Excellent molecular graphics package with  support for a wide range of operations, including flexible molecular graphics, high resolution images for publication, user-driven analysis, multiple sequence alignment analysis, multiple model analysis, dockin
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* [http://fedoraproject.org/ Fedora]
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* [[Clann]] - Clann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree  analysis (which are used as optimality criteria) and allows exhaustive and  heuristic searches of tree-space to find the best supertree
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* [[Clustal W]] - The famous multiple alignment program
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* [[Clustal X]] - Provides a window-based user interface to the Clustal W multiple alignment program
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* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
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* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
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* [[ConsInspector]] - A tool for the prediction of protein binding sites in nucleic acids
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* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
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===D===
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==See also==
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* [[DBWatcher]] - DBWatcher is a program handling periodic [[BLAST]] searches to find similarities to your own sequences.
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* [[:Category:Software]]
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* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
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* [[Research and development topics]] (including links to software)
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* [[Deep View Swiss-PdbViewer]] - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time
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* [[Bioinformatics FAQ]]
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* [[DIALIGN]] - DIALIGN is an alignment program that relies on comparison of whole segments of the sequences instead of comparison of single residue
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* [[DINO]] - a realtime 3D visualization program for structural biology data.
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* [[DNA-GUI]] - DNA Graphical User Interface
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* [[DomainFinder]] - DomainFinder 1.0  DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins
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===E===
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For a list of software (derived from [[SEQwiki]]), click here [[Software/list]].
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* [[EMBOSS]] - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
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==External links==
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* [[Ensembl]] - software system which produces and maintains automatic annotation on eukaryoticgenomes
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===F===
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* [http://www.bioinformatics.org/software/mol_linux.php3 Molecular Linux (original listing)]
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* [http://www.facebook.com/pages/SeqChallange/217316754955635 SeqChallenge]
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* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
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* [http://in-silico.net In-Silico Online] Online bioinformatic tools
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* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
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===G===
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* [[Garlic]] - a free molecular visualization program
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* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
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* [[GDE]] -  The GDE is a set of programs for multiple sequence alignment and analysis.
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* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems
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* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
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* [[geneid]] -  Gene prediction tool, it can also introduce homology and annotation evidences and produce a reannotation of a genomic sequence. A pthreads parallel version also available.
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* [[GeneView II]] - Interactive GenBank Entry Visualization
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* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
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* [[GenomePixelizer]] - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
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* [[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
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* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
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* [[GRIL]] - GRIL automates the process of identifying large-scale genome inversions and rearrangements
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* [[Gromacs]] - The World' s fastest Molecular Dynamics - and it' s GPL
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* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis
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===H===
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* [[HMMER]] - Profile hidden Markov models for biological sequence analysis
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===I===
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* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
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===J===
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* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
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* [[Jalview]] - Jalview - a java multiple alignment editor
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===K===
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* [[Kintecus]] -  Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
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===L===
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* [[Leksbot]] - an explanatory dictionary of botanic and biological terms
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* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
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* [[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.
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===M===
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* [[MAExplorer]] - The Microarray Explorer (MAExplorer) is a Java-based data-mining facility for microarray databases run as a stand-alone program. It includes graphics, statistics, clustering, reports, data filtering.
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* [[Mauve]] - Mauve is a multiple genome alignment and visualization package that  considers large-scale rearrangements in addition to nucleotide substitution and indels.
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* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
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* [[MeltSim]] - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake.
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* [[MMTK-2.2]] - molecular modeling tool-kit 2.2
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* [[MODELLER]] - a program for homology protein structure modelling by satisfaction of spatial restraints.
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* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
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* [[MOLPHY]] - A Computer Program Package for Molecular Phylogenetics including ProtML
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* [[MOPAC7]] - a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
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* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
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* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
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* [[MSPcrunch]] - a [[BLAST]] enhancement filter
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* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
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* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
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* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
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* [[NCRNASCAN]] - a structural RNA genefinder
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* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
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===O===
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* [[OmniGene]] - Standardizing Biological Data Interchange Through Web Services Technology
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* [[On-line Genome Annotations]] - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features
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* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
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===P===
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* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
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* [[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
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* [[Paup]] - Software package for inference of evolutionary trees
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* [[PHASE]] - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
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* [[phrap]] - a program for assembling shotgun DNA sequence data
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* [[phred]] - Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
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* [[PHYLIP]] - PHYLIP is a free package of programs for inferring phylogenies.
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* [[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
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* [[PhyloGrapher]] - PhyloGrapher is a program designed to visualize and study evolutional relationship between families of homologous genes or proteins. PhyloGrapher is a drawing tool that generates custom graphs out of the given set of genes based on distance matrix file.
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* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
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* [[PKNOTS]] - RNA pseudoknot prediction
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* [[Populations]] - Population genetic software (individuals or populations distances, phylogenetic trees)
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* [[Pratt]] - a pattern discovery tool
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* [[primer]] - a program for picking primers for PCR reaction
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* [[ProSA]] - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching
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* [[PyMol]] - PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
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* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
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===R===
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* [[rasmol]] - RasMol is a free program which displays molecular structure.
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* [[readseq]] - Reads and writes nucleic/protein sequences in various format
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* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
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* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher
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* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
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===S===
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* [[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
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* [[SEALS]] - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
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* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
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* [[SEPON]] - SEPON designs gene-specific oligonucleotides for microarray experiments and is able to use EST input from organisms in which the genome is not annotated for genes. SEPON implements a novel algorithm for reducing cross-hybridization by utilizing thermodyna
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* [[SeqPup]] - SeqPup biological sequence editor and analysis program
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* [[ShadyBox]] - The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
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* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
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* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
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* [[Spock]] - a full-featured molecular graphics program
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* [[Staden Package]] - This is a free to academics (charge for commercial users) package including sequence assemble, trace viewing/editing and sequence analysis tools. It also includes a GUI to the free EMBOSS suite.
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* [[Steric]] - A Program to Calculate the Steric Size of Molecules about a Point in terms of their Cone Angles and Solid Angles, as well as their total Volumes and Projected Areas
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* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
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* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.
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* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
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* [[TREE-PUZZLE]] - Maximum likelihood analysis for nucleotide, amino acid, and two-state data
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* [[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.
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===U===
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* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
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* [[unrooted]] - Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.
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===V===
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* [[VEGA]] - VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D struct
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* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd
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* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison
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* [[VMD]] - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
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===W===
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* [[WHAT IF]] - WHAT  IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc
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* [[WU-Blast]] - Washington U. [[BLAST]]
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===X===
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* [[XMolCalc]] - a small utility that allows you to calculate a molecular weight
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* [[xsact]] - EST clustering tool
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===Z===
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* [[ZDOCK]] - Protein-protein complex structure prediction software
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Revision as of 11:55, 28 July 2011

Contents

Popular software for bioinformatics

Everyday bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHAT IF.

More:

Popular Linux OS distributions for bioinformatics

Generic yet popular distributions:

See also

For a list of software (derived from SEQwiki), click here Software/list.

External links

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