Software

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===3D structure visualization===
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== Popular software for bioinformatics ==
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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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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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===Applied Biosystems (ABI)===
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More:
 +
* [[NetSurfP]] - Protein Surface Accessibility and Secondary Structure Predictions
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* [[NetTurnP]] - Prediction of Beta-turn regions in protein sequences
 +
* [[MODELLER]] - Used for homology or comparative modeling of protein three-dimensional structures
 +
* [http://autodock.scripps.edu/ AutoDock] - Suite of Automated Docking Tools
 +
* [http://www.gromacs.org/ Gromacs] - A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids
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* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
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==  Popular Linux OS distributions for bioinformatics ==
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* [[phrap]] - a program for assembling shotgun DNA sequence data
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* [http://www.gentoo.org/ Gentoo Linux] ([http://packages.gentoo.org/category/sci-biology?full_cat List of bioinformatics packages])
 +
* [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]
 +
* [http://opendiscovery.org.in Open Discovery] - An integrative bioinformatics linux distro with high performance computing capability
 +
* [http://www.bioslax.com/ Bioslax]
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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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Generic yet popular distributions:
 +
* [http://www.ubuntu.com/ Ubuntu]
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* [http://fedoraproject.org/ Fedora]
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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. 
+
==See also==
-
===Affine gap===
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* [[:Category:Software]]
 +
* [[Research and development topics]] (including links to software)
 +
* [[Bioinformatics FAQ]]
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* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.  
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For a list of software (derived from [[SEQwiki]]), click here [[Software/list]].
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===Alignment===
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==External links==
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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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* [http://www.bioinformatics.org/software/mol_linux.php3 Molecular Linux (original listing)]
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* [[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
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* [http://www.facebook.com/pages/SeqChallange/217316754955635 SeqChallenge]
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* [[clustalw]] - The famous ClustalW multiple alignment program
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* [http://in-silico.net In-Silico Online] Online bioinformatic tools
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* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
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* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
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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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* [[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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* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
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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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* [[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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* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
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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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* [[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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* [[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
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
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* [[ShadyBox]] - ShadyBox The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
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* [[xsact]] - EST clustering tool
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-
 
+
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===Amplification===
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+
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* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
-
 
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===Analytical ultracentrifugation===
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+
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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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===Aneda===
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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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-
 
+
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===Assembly===
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-
 
+
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* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[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.
+
-
 
+
-
===Base calling===
+
-
 
+
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* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
+
-
* [[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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===Bayesian methods===
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-
 
+
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* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
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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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+
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===BioCoRE===
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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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===BLAST===
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-
 
+
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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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* [[DBWatcher]] - DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.
+
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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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* [[MSPcrunch]] - a BLAST enhancement filter
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* [[WU-Blast]] - Washington U. [[BLAST]]
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===C. elegans===
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* [[Angler]] - A Browser of ''C. elegans'' Embryo Development In Time and Space
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===CASP===
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* [[LIBELLULA]] - A neural network based web server to evaluate fold recognition results
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===Chemical kinetics===
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* [[Kintecus]] -  Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
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===Chemical structures===
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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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===Chromatogram===
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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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* [[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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+
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===Code generators===
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* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
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===Comparative analysis===
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* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
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+
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===Comparative genetics===
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+
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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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===Composition===
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* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
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===Correlation===
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* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
+
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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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+
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===Crystallography===
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* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
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===Data analysis===
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+
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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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+
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===Data flow===
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+
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* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
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===Data mining===
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+
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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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+
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===Databases===
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* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project
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* [[ARB]] - Microbiologist's sequence database tool
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* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
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* [[HMMER]] - Profile hidden Markov models for biological sequence analysis
+
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* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[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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===Database interface===
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-
 
+
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* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
+
-
 
+
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===Database searching===
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+
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* [[HMMER]] - Profile hidden Markov models for biological sequence analysis 
+
-
 
+
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===Database segmentation===
+
-
 
+
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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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===Denaturation===
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-
 
+
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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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+
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===Dictionaries===
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+
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* [[Leksbot]] - an explanatory dictionary of botanic and biological terms
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+
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===Distance correlations===
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+
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* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
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-
 
+
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===DNA sequence viewer===
+
-
 
+
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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.
+
-
 
+
-
===DNA sequencing===
+
-
 
+
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[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.
+
-
 
+
-
===DNA structure===
+
-
 
+
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* [[Garlic]] - a free molecular visualization program
+
-
 
+
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===Drawing===
+
-
 
+
-
* [[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
+
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
 
+
-
===Duplications===
+
-
 
+
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* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
+
-
* [[GenomePixelizer]] - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
+
-
* [[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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===Electron density maps===
+
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+
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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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===EMBL===
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* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
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* [[phrap]] - a program for assembling shotgun DNA sequence data
+
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* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
+
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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.
+
-
 
+
-
===EMBOSS===
+
-
 
+
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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.
+
-
 
+
-
===EST===
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+
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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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* [[xsact]] - EST clustering tool
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===EST clustering similarity alignment===
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* [[xsact]] - EST clustering tool
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===EVA===
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* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis
+
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* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
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===Evolution===
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-
 
+
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* [[GenomePixelizer]] - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
+
-
* [[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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===Exons===
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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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===Extensions===
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* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
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===File conversion===
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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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+
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===Finite elements===
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-
 
+
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* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
-
 
+
-
===Fold recognition===
+
-
 
+
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* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
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===Format converters===
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* [[Babel]] - a program designed to interconvert a number of  file formats currently used in molecular modeling
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===GenBank entry visualization===
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* [[GeneView II]] - Interactive GenBank Entry Visualization
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===Gene duplications===
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* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
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+
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===Gene expression===
+
-
 
+
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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.
+
-
* [[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
+
-
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
+
-
 
+
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===Gene finding===
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* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd
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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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+
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===Gene regulation===
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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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===Genetic distances===
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* [[Populations]] - Population genetic software (individuals or populations distances, phylogenetic trees)
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===Genome annotation===
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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.
+
-
* [[Ensembl]] - software system which produces and maintains automatic annotation on eukaryoticgenomes
+
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* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
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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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+
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===Genome development libraries===
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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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+
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===Genome rearrangement===
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+
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* [[GRIL]] - GRIL automates the process of identifying large-scale genome inversions and rearrangements
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===Genome retrieval===
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* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis
+
-
 
+
-
===Genomic database system===
+
-
 
+
-
* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project
+
-
 
+
-
===Genomics===
+
-
 
+
-
* [[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 supert
+
-
* [[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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+
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===GFF===
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-
 
+
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* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
+
-
 
+
-
===Global fitting===
+
-
 
+
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
-
 
+
-
===Graph theory===
+
-
 
+
-
* [[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.
+
-
 
+
-
===grep===
+
-
 
+
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
-
 
+
-
===Group-specific primers===
+
-
 
+
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
-
 
+
-
===Hidden Markov Models===
+
-
 
+
-
* [[HMMER]] - Profile hidden Markov models for biological sequence analysis
+
-
* [[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
+
-
* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd
+
-
 
+
-
===Homologous genes===
+
-
 
+
-
* [[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.
+
-
 
+
-
===Inference===
+
-
 
+
-
* [[MOLPHY]] - A Computer Program Package for Molecular Phylogenetics including ProtML
+
-
* [[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.
+
-
 
+
-
===Java===
+
-
 
+
-
* [[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.
+
-
* [[BioJava]] - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
+
-
* [[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.
+
-
 
+
-
===Libraries===
+
-
 
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[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.
+
-
 
+
-
===Maximum likelihood===
+
-
 
+
-
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
+
-
* [[MOLPHY]] - A Computer Program Package for Molecular Phylogenetics including ProtML
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[TREE-PUZZLE]] - Maximum likelihood analysis for nucleotide, amino acid, and two-state data
+
-
 
+
-
===MCMC===
+
-
 
+
-
* [[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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===Medline===
+
-
 
+
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* [[BioMail]] - automate searching for recent scientific papers in the PubMed Medline database
+
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+
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===Melting temperature===
+
-
 
+
-
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
+
-
* [[MeltSim]] - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake. 
+
-
 
+
-
===Microarray analysis===
+
-
 
+
-
* [[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.
+
-
* [[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
+
-
* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.
+
-
 
+
-
===Modeling===
+
-
 
+
-
* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.
+
-
* [[Kintecus]] -  Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
+
-
* [[MMTK-2.2]] - molecular modeling tool-kit 2.2
+
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
* [[WHAT IF]] - WHAT  IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc
+
-
 
+
-
===Molecular dynamics===
+
-
 
+
-
* [[Gromacs]] - The World' s fastest Molecular Dynamics - and it' s gpl
+
-
* [[MMTK-2.2]] - molecular modeling tool-kit 2.2
+
-
* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems
+
-
 
+
-
===Molecular editors===
+
-
 
+
-
* [[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.
+
-
 
+
-
===Molecular graphics===
+
-
 
+
-
* [[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, docking
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
* [[Spock]] - a full-featured molecular graphics program
+
-
 
+
-
===Molecular mechanics===
+
-
 
+
-
* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.
+
-
 
+
-
===Molecular modeling===
+
-
 
+
-
* [[Babel]] - a program designed to interconvert a number of  file formats currently used in molecular modeling
+
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
* [[WHAT IF]] - WHAT  IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc
+
-
 
+
-
===Molecular simulations===
+
-
 
+
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
 
+
-
===Molecular structure analysis===
+
-
 
+
-
* [[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
+
-
 
+
-
===Molecular visualization===
+
-
 
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[rasmol]] - RasMol is a free program which displays molecular structure.
+
-
* [[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
+
-
* [[VMD]] - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
+
-
 
+
-
===Molecular weight===
+
-
 
+
-
* [[XMolCalc]] - a small utility that allows you to calculate a molecular weight
+
-
 
+
-
===Monte Carlo===
+
-
 
+
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
-
 
+
-
===Motifs===
+
-
 
+
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
-
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher
+
-
 
+
-
===MPI===
+
-
 
+
-
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
+
-
 
+
-
===Multiple===
+
-
 
+
-
* [[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, docking
+
-
* [[clustalw]] - The famous ClustalW multiple alignment program
+
-
* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
+
-
* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[Jalview]] - Jalview - a java multiple alignment editor
+
-
* [[Mauve]] - Mauve is a multiple genome alignment and visualization package that  considers large-scale rearrangements in addition to nucleotide substitution and indels.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
 
+
-
===Multiple alignment editors===
+
-
 
+
-
* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
+
-
* [[Jalview]] - Jalview - a java multiple alignment editor
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
 
+
-
===Multiple genome alignment===
+
-
 
+
-
* [[Mauve]] - Mauve is a multiple genome alignment and visualization package that  considers large-scale rearrangements in addition to nucleotide substitution and indels.
+
-
 
+
-
===Multiple protein structure visualization===
+
-
 
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
 
+
-
===Multiple sequence alignment===
+
-
 
+
-
* [[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
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
 
+
-
===Multiple sequence alignment drawing===
+
-
 
+
-
* [[ShadyBox]] - The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
 
+
-
===MySQL===
+
-
 
+
-
* [[Ensembl]] - software system which produces and maintains automatic annotation on eukaryoticgenomes
+
-
 
+
-
===NAMD===
+
-
 
+
-
* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
+
-
 
+
-
===Neural networks===
+
-
 
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
+
-
 
+
-
===NMR===
+
-
 
+
-
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
+
-
 
+
-
===Nucleic acids===
+
-
 
+
-
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
+
-
 
+
-
===Oligonucleotides===
+
-
 
+
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
-
* [[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
+
-
 
+
-
===Online searching===
+
-
 
+
-
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
+
-
 
+
-
===Online tools===
+
-
 
+
-
* [[On-line Genome Annotations]] - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features
+
-
 
+
-
===Parallel===
+
-
 
+
-
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
+
-
 
+
-
===Patterns===
+
-
 
+
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[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
+
-
* [[Pratt]] - a pattern discovery tool
+
-
 
+
-
===PCR===
+
-
 
+
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
-
 
+
-
===PDB===
+
-
 
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[MMTK-2.2]] - molecular modeling tool-kit 2.2
+
-
 
+
-
===Perl===
+
-
 
+
-
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
+
-
 
+
-
===Phase===
+
-
 
+
-
* [[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.
+
-
 
+
-
===Phenotype analysis===
+
-
 
+
-
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
+
-
 
+
-
===Phylogenetics===
+
-
 
+
-
* [[ATV]] - a phylogenetic tree display tool
+
-
* [[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 supert
+
-
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[MOLPHY]] - A Computer Program Package for Molecular Phylogenetics including ProtML
+
-
* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[Paup]] - Software package for inference of evolutionary trees
+
-
* [[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.
+
-
* [[PHYLIP]] - PHYLIP is a free package of programs for inferring phylogenies.
+
-
* [[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
+
-
* [[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.
+
-
* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
* [[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. 
+
-
 
+
-
===Phylogenetic trees===
+
-
 
+
-
* [[ATV]] - a phylogenetic tree display tool
+
-
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
+
-
* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[Paup]] - Software package for inference of evolutionary trees
+
-
* [[PHYLIP]] - PHYLIP is a free package of programs for inferring phylogenies.
+
-
* [[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
+
-
* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
* [[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. 
+
-
 
+
-
===Phylogenetic tree reconstruction===
+
-
 
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
 
+
-
===Phylogenomics===
+
-
 
+
-
* [[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 supert
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
 
+
-
===PostScript===
+
-
 
+
-
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
+
-
 
+
-
===POV-Ray===
+
-
 
+
-
* [[Deep View Swiss-PdbViewer]] - Swiss-PdbViewer is an application that provides a user          friendly interface allowing to analyse several proteins at the same time
+
-
 
+
-
===Prediction===
+
-
 
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[ConsInspector]] - A tool for the prediction of protein binding sites in nucleic acids
+
-
* [[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.
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
-
===Primers===
+
-
 
+
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
-
* [[primer]] - a program for picking primers for PCR reaction
+
-
 
+
-
===PROSITE===
+
-
 
+
-
* [[ProSA]] - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching
+
-
 
+
-
===Protein binding sites===
+
-
 
+
-
* [[ConsInspector]] - A tool for the prediction of protein binding sites in nucleic acids
+
-
 
+
-
===Protein docking===
+
-
 
+
-
* [[ZDOCK]] - Protein-protein complex structure prediction software
+
-
 
+
-
===Protein domains===
+
-
 
+
-
* [[DomainFinder]] - DomainFinder 1.0  DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins
+
-
* [[ProSA]] - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching
+
-
 
+
-
===Protein families===
+
-
 
+
-
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
+
-
 
+
-
===Protein interaction===
+
-
 
+
-
* [[ZDOCK]] - Protein-protein complex structure prediction software
+
-
 
+
-
===Protein modelling===
+
-
 
+
-
* [[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
+
-
 
+
-
===Protein structure===
+
-
 
+
-
* [[Abacus]] - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
* [[MODELLER]] - a program for homology protein structure modelling by satisfaction of spatial restraints.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
 
+
-
===Protein structure prediction===
+
-
 
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
-
===Protein/DNA/RNA family clustering===
+
-
 
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
 
+
-
===PubMed===
+
-
 
+
-
* [[BioMail]] - automate searching for recent scientific papers in the PubMed Medline database
+
-
 
+
-
===Python===
+
-
 
+
-
* [[Biopython]] - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
 
+
-
===Real-time visualization===
+
-
 
+
-
* [[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.
+
-
 
+
-
===Reannotation===
+
-
 
+
-
* [[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.
+
-
 
+
-
===Regular expressions===
+
-
 
+
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
-
 
+
-
===Regulatory sequence analysis===
+
-
 
+
-
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
+
-
 
+
-
===Rendered animations===
+
-
 
+
-
* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems
+
-
 
+
-
===RNA===
+
-
 
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
+
-
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[NCRNASCAN]] - a structural RNA genefinder
+
-
* [[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.
+
-
* [[PKNOTS]] - RNA pseudoknot prediction
+
-
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
+
-
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher
+
-
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
+
-
* [[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.
+
-
* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison
+
-
 
+
-
===RNA folding===
+
-
 
+
-
* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison
+
-
 
+
-
===RNA gene finder===
+
-
 
+
-
* [[NCRNASCAN]] - a structural RNA genefinder
+
-
 
+
-
===RNA motif===
+
-
 
+
-
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher
+
-
 
+
-
===RNA pseudoknots===
+
-
 
+
-
* [[PKNOTS]] - RNA pseudoknot prediction
+
-
 
+
-
===RNA secondary structure===
+
-
 
+
-
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
+
-
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
+
-
 
+
-
===SCF===
+
-
 
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[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.
+
-
 
+
-
===Secondary structure===
+
-
 
+
-
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
+
-
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
+
-
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
+
-
 
+
-
===SEPON===
+
-
 
+
-
* [[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
+
-
 
+
-
===Sequences===
+
-
 
+
-
* [[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]]
+
-
 
+
-
===Sequence alignment===
+
-
 
+
-
* [[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
+
-
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
+
-
* [[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
+
-
* [[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
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
 
+
-
===Sequence analysis===
+
-
 
+
-
* [[ARB]] - Microbiologist's sequence database tool
+
-
* [[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
+
-
* [[clustalw]] - The famous ClustalW multiple alignment program
+
-
* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
+
-
* [[DNA-GUI]] - DNA Graphical User Interface
+
-
* [[EMBOSS]] - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
+
-
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
+
-
* [[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
+
-
* [[PKNOTS]] - RNA pseudoknot prediction
+
-
* [[Pratt]] - a pattern discovery tool
+
-
* [[readseq]] - Reads and writes nucleic/protein sequences in various format
+
-
* [[SEALS]] - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
+
-
* [[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]]
+
-
 
+
-
===Sequence comparisons===
+
-
 
+
-
* [[DBWatcher]] - DBWatcher is a program handling periodic [[BLAST]] searches to find similarities to your own sequences.
+
-
 
+
-
===Sequence conversion===
+
-
 
+
-
* [[readseq]] - Reads and writes nucleic/protein sequences in various format
+
-
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
+
-
 
+
-
===Sequence databases===
+
-
 
+
-
* [[ARB]] - Microbiologist's sequence database tool
+
-
 
+
-
===Sequence editor===
+
-
 
+
-
* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
+
-
* [[SeqPup]] - SeqPup biological sequence editor and analysis program
+
-
 
+
-
===Sequence finishing===
+
-
 
+
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
-
 
+
-
===Sequence patterns===
+
-
 
+
-
* [[Pratt]] - a pattern discovery tool
+
-
 
+
-
===Sequence similarity===
+
-
 
+
-
* [[BLAST]] - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
+
-
 
+
-
===Sequence utilities===
+
-
 
+
-
* [[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
+
-
 
+
-
===Sequencing===
+
-
 
+
-
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
+
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[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.
+
-
 
+
-
===Smith-Waterman===
+
-
 
+
-
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
+
-
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
+
-
 
+
-
===Solid Angle calculation===
+
-
 
+
-
* [[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
+
-
 
+
-
===Statistical mechanics===
+
-
 
+
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
 
+
-
===Steric size calculation===
+
-
 
+
-
* [[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
+
-
 
+
-
===Structural alignments===
+
-
 
+
-
* [[Deep View Swiss-PdbViewer]] - Swiss-PdbViewer is an application that provides a user          friendly interface allowing to analyse several proteins at the same time
+
-
 
+
-
===Structural biology===
+
-
 
+
-
* [[DINO]] - a realtime 3D visualization program for structural biology data.
+
-
 
+
-
===Structure===
+
-
 
+
-
* [[Abacus]] - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
+
-
* [[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
+
-
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
+
-
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
* [[MODELLER]] - a program for homology protein structure modelling by satisfaction of spatial restraints.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[MOPAC7]] - a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
+
-
* [[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.
+
-
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
+
-
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
+
-
 
+
-
===Structure analysis===
+
-
 
+
-
* [[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
+
-
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
+
-
 
+
-
===Structure prediction===
+
-
 
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
-
===Substitution===
+
-
 
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[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.
+
-
 
+
-
===Substitution rates===
+
-
 
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
 
+
-
===SwissProt===
+
-
 
+
-
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
+
-
 
+
-
===Tcl/Tk===
+
-
 
+
-
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
+
-
 
+
-
===Thermodynamics===
+
-
 
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
+
-
 
+
-
===Threading===
+
-
 
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
-
===Trace===
+
-
 
+
-
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[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.
+
-
* [[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.
+
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
-
 
+
-
===Trace chromatogram===
+
-
 
+
-
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
+
-
 
+
-
===Trace files===
+
-
 
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[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.
+
-
 
+
-
===Trajectory analysis===
+
-
 
+
-
* [[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
+
-
 
+
-
===Transcription factors===
+
-
 
+
-
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
+
-
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
+
-
 
+
-
===Trees===
+
-
 
+
-
* [[ATV]] - a phylogenetic tree display tool
+
-
* [[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 supert
+
-
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[Paup]] - Software package for inference of evolutionary trees
+
-
* [[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.
+
-
* [[PHYLIP]] - PHYLIP is a free package of programs for inferring phylogenies.
+
-
* [[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
+
-
* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
* [[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. 
+
-
 
+
-
===Tree of life===
+
-
 
+
-
* [[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.
+
-
 
+
-
===Tree viewers===
+
-
 
+
-
* [[ATV]] - a phylogenetic tree display tool
+
-
* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
+
-
* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
+
-
* [[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. 
+
-
 
+
-
===tRNA searching===
+
-
 
+
-
* [[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.
+
-
 
+
-
===Visualization===
+
-
 
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[GeneView II]] - Interactive GenBank Entry Visualization
+
-
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[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.
+
-
* [[rasmol]] - RasMol is a free program which displays molecular structure.
+
-
* [[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
+
-
* [[VMD]] - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
+
-
 
+
-
===VMD===
+
-
 
+
-
* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. 
+
-
 
+
-
===Web robots===
+
-
 
+
-
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
+
-
 
+
-
===Workflow===
+
-
 
+
-
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
+

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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