Software

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===3D structure visualization===
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==3D structure 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.  
* [[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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===Applied Biosystems (ABI)===
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==Applied Biosystems (ABI)==
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
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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.   
* [[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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===Affine gap===
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==Affine gap==
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.  
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.  
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===Alignment===
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==Alignment==
* [[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.
* [[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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* [[xsact]] - EST clustering tool  
* [[xsact]] - EST clustering tool  
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===Amplification===
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==Amplification==
* [[Amplicon]] - Program for designing group-specific PCR primer sets  
* [[Amplicon]] - Program for designing group-specific PCR primer sets  
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===Analytical ultracentrifugation===
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==Analytical ultracentrifugation==
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
* [[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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==Aneda==
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
* [[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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===Assembly===
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==Assembly==
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
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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.  
* [[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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===Base calling===
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==Base calling==
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
* [[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.  
* [[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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==Bayesian methods==
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood  
* [[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.  
* [[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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===BioCoRE===
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==BioCoRE==
* [[NAMD]] - NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.   
* [[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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==BLAST==
* [[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.
* [[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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* [[WU-Blast]] - Washington U. [[BLAST]]  
* [[WU-Blast]] - Washington U. [[BLAST]]  
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===C. elegans===
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==C. elegans==
* [[Angler]] - A Browser of ''C. elegans'' Embryo Development In Time and Space  
* [[Angler]] - A Browser of ''C. elegans'' Embryo Development In Time and Space  
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===CASP===
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==CASP==
* [[LIBELLULA]] - A neural network based web server to evaluate fold recognition results  
* [[LIBELLULA]] - A neural network based web server to evaluate fold recognition results  
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===Chemical kinetics===
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==Chemical kinetics==
* [[Kintecus]] -  Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions  
* [[Kintecus]] -  Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions  
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===Chemical structures===
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==Chemical structures==
* [[MOPAC7]] - a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.  
* [[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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==Chromatogram==
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
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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.  
* [[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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===Code generators===
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==Code generators==
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.  
* [[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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==Comparative analysis==
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences  
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences  
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===Comparative genetics===
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==Comparative genetics==
* [[GenomePixelizer]] - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.  
* [[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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==Composition==
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences  
* [[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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==Correlation==
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
* [[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.  
* [[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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===Crystallography===
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==Crystallography==
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis  
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis  
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===Data analysis===
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==Data analysis==
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
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===Data flow===
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==Data flow==
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.  
* [[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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==Data mining==
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.  
* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.  
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===Databases===
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==Databases==
* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project
* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project
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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.  
* [[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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==Database interface==
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
* [[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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==Database searching==
* [[HMMER]] - Profile hidden Markov models for biological sequence analysis   
* [[HMMER]] - Profile hidden Markov models for biological sequence analysis   
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===Database segmentation===
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==Database segmentation==
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.  
* [[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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==Denaturation==
* [[MeltSim]] - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake.   
* [[MeltSim]] - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake.   
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===Dictionaries===
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==Dictionaries==
* [[Leksbot]] - an explanatory dictionary of botanic and biological terms  
* [[Leksbot]] - an explanatory dictionary of botanic and biological terms  
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===Distance correlations===
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==Distance correlations==
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences  
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences  
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===DNA sequence viewer===
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==DNA sequence viewer==
* [[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.  
* [[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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===DNA sequencing===
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==DNA sequencing==
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
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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.  
* [[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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===DNA structure===
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==DNA structure==
* [[Garlic]] - a free molecular visualization program  
* [[Garlic]] - a free molecular visualization program  
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===Drawing===
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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
* [[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  
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms  
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===Duplications===
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==Duplications==
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
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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.  
* [[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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==Electron density maps==
* [[Deep View Swiss-PdbViewer]] - Swiss-PdbViewer is an application that provides a user          friendly interface allowing to analyse several proteins at the same time  
* [[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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==EMBL==
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
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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.  
* [[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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===EMBOSS===
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==EMBOSS==
* [[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.  
* [[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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===EST===
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==EST==
* [[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
* [[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
* [[xsact]] - EST clustering tool  
* [[xsact]] - EST clustering tool  
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===EST clustering similarity alignment===
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==EST clustering similarity alignment==
* [[xsact]] - EST clustering tool  
* [[xsact]] - EST clustering tool  
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===EVA===
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==EVA==
* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis
* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
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===Evolution===
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==Evolution==
* [[GenomePixelizer]] - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
* [[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.  
* [[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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==Exons==
* [[Abacus]] - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of 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.  
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===Extensions===
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==Extensions==
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language  
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language  
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===File conversion===
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==File conversion==
* [[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  
* [[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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===Finite elements===
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==Finite elements==
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
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===Fold recognition===
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==Fold recognition==
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
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===Format converters===
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==Format converters==
* [[Babel]] - a program designed to interconvert a number of  file formats currently used in molecular modeling  
* [[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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==GenBank entry visualization==
* [[GeneView II]] - Interactive GenBank Entry Visualization  
* [[GeneView II]] - Interactive GenBank Entry Visualization  
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===Gene duplications===
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==Gene duplications==
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER  
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER  
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===Gene expression===
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==Gene expression==
* [[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.
* [[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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* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
* [[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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==Gene finding==
* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd  
* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd  
* [[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.  
* [[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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===Gene regulation===
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==Gene regulation==
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.  
* [[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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==Genetic distances==
* [[Populations]] - Population genetic software (individuals or populations distances, phylogenetic trees)  
* [[Populations]] - Population genetic software (individuals or populations distances, phylogenetic trees)  
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===Genome annotation===
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==Genome annotation==
* [[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.
* [[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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* [[On-line Genome Annotations]] - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features  
* [[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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===Genome development libraries===
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==Genome development libraries==
* [[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.
* [[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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===Genome rearrangement===
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==Genome rearrangement==
* [[GRIL]] - GRIL automates the process of identifying large-scale genome inversions and rearrangements
* [[GRIL]] - GRIL automates the process of identifying large-scale genome inversions and rearrangements
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===Genome retrieval===
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==Genome retrieval==
* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis  
* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis  
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===Genomic database system===
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==Genomic database system==
* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project  
* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project  
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===Genomics===
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==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
* [[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.  
* [[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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===GFF===
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==GFF==
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript  
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript  
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===Global fitting===
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==Global fitting==
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
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===Graph theory===
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==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.  
* [[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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===grep===
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==grep==
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.  
* [[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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===Group-specific primers===
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==Group-specific primers==
* [[Amplicon]] - Program for designing group-specific PCR primer sets  
* [[Amplicon]] - Program for designing group-specific PCR primer sets  
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===Hidden Markov Models===
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==Hidden Markov Models==
* [[HMMER]] - Profile hidden Markov models for biological sequence analysis  
* [[HMMER]] - Profile hidden Markov models for biological sequence analysis  
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* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd  
* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd  
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===Homologous genes===
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==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.  
* [[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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===Inference===
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==Inference==
* [[MOLPHY]] - A Computer Program Package for Molecular Phylogenetics including ProtML
* [[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.  
* [[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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===Java===
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==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.
* [[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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* [[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.  
* [[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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===Libraries===
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==Libraries==
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
* [[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.  
* [[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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===Maximum likelihood===
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==Maximum likelihood==
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
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* [[TREE-PUZZLE]] - Maximum likelihood analysis for nucleotide, amino acid, and two-state data  
* [[TREE-PUZZLE]] - Maximum likelihood analysis for nucleotide, amino acid, and two-state data  
-
===MCMC===
+
==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.  
* [[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.  
-
===Medline===
+
==Medline==
* [[BioMail]] - automate searching for recent scientific papers in the PubMed Medline database  
* [[BioMail]] - automate searching for recent scientific papers in the PubMed Medline database  
-
===Melting temperature===
+
==Melting temperature==
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex  
* [[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.   
* [[MeltSim]] - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake.   
-
===Microarray analysis===
+
==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.
* [[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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* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.  
* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.  
-
===Modeling===
+
==Modeling==
* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.
* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.
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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  
* [[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===
+
==Molecular dynamics==
* [[Gromacs]] - The World' s fastest Molecular Dynamics - and it' s gpl  
* [[Gromacs]] - The World' s fastest Molecular Dynamics - and it' s gpl  
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* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems  
* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems  
-
===Molecular editors===
+
==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.  
* [[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===
+
==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
* [[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
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* [[Spock]] - a full-featured molecular graphics program  
* [[Spock]] - a full-featured molecular graphics program  
-
===Molecular mechanics===
+
==Molecular mechanics==
* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.  
* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.  
-
===Molecular modeling===
+
==Molecular modeling==
* [[Babel]] - a program designed to interconvert a number of  file formats currently used in molecular modeling  
* [[Babel]] - a program designed to interconvert a number of  file formats currently used in molecular modeling  
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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  
* [[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===
+
==Molecular simulations==
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.  
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.  
-
===Molecular structure analysis===
+
==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  
* [[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===
+
==Molecular visualization==
* [[Garlic]] - a free molecular visualization program
* [[Garlic]] - a free molecular visualization program
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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  
* [[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===
+
==Molecular weight==
* [[XMolCalc]] - a small utility that allows you to calculate a molecular weight  
* [[XMolCalc]] - a small utility that allows you to calculate a molecular weight  
-
===Monte Carlo===
+
==Monte Carlo==
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
-
===Motifs===
+
==Motifs==
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
* [[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  
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher  
-
===MPI===
+
==MPI==
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.  
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.  
-
===Multiple===
+
==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
* [[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
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* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms  
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms  
-
===Multiple alignment editors===
+
==Multiple alignment editors==
* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
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* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
-
===Multiple genome alignment===
+
==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.  
* [[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===
+
==Multiple protein structure visualization==
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
-
===Multiple sequence alignment===
+
==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
* [[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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* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
-
===Multiple sequence alignment drawing===
+
==Multiple sequence alignment drawing==
* [[ShadyBox]] - The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms  
* [[ShadyBox]] - The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms  
-
===MySQL===
+
==MySQL==
* [[Ensembl]] - software system which produces and maintains automatic annotation on eukaryoticgenomes  
* [[Ensembl]] - software system which produces and maintains automatic annotation on eukaryoticgenomes  
-
===NAMD===
+
==NAMD==
* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
-
===Neural networks===
+
==Neural networks==
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
* [[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  
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences  
-
===NMR===
+
==NMR==
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis  
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis  
-
===Nucleic acids===
+
==Nucleic acids==
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex  
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex  
-
===Oligonucleotides===
+
==Oligonucleotides==
* [[Amplicon]] - Program for designing group-specific PCR primer sets
* [[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  
* [[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===
+
==Online searching==
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.  
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.  
-
===Online tools===
+
==Online tools==
* [[On-line Genome Annotations]] - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features  
* [[On-line Genome Annotations]] - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features  
-
===Parallel===
+
==Parallel==
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.  
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.  
-
===Patterns===
+
==Patterns==
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
* [[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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* [[Pratt]] - a pattern discovery tool  
* [[Pratt]] - a pattern discovery tool  
-
===PCR===
+
==PCR==
* [[Amplicon]] - Program for designing group-specific PCR primer sets  
* [[Amplicon]] - Program for designing group-specific PCR primer sets  
-
===PDB===
+
==PDB==
* [[Garlic]] - a free molecular visualization program
* [[Garlic]] - a free molecular visualization program
* [[MMTK-2.2]] - molecular modeling tool-kit 2.2  
* [[MMTK-2.2]] - molecular modeling tool-kit 2.2  
-
===Perl===
+
==Perl==
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER  
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER  
-
===Phase===
+
==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.  
* [[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===
+
==Phenotype analysis==
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)  
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)  
-
===Phylogenetics===
+
==Phylogenetics==
* [[ATV]] - a phylogenetic tree display tool
* [[ATV]] - a phylogenetic tree display tool
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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.   
* [[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===
+
==Phylogenetic trees==
* [[ATV]] - a phylogenetic tree display tool
* [[ATV]] - a phylogenetic tree display tool
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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.   
* [[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===
+
==Phylogenetic tree reconstruction==
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood  
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood  
-
===Phylogenomics===
+
==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
* [[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.  
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.  
-
===PostScript===
+
==PostScript==
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript  
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript  
-
===POV-Ray===
+
==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  
* [[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===
+
==Prediction==
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
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* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
-
===Primers===
+
==Primers==
* [[Amplicon]] - Program for designing group-specific PCR primer sets
* [[Amplicon]] - Program for designing group-specific PCR primer sets
* [[primer]] - a program for picking primers for PCR reaction  
* [[primer]] - a program for picking primers for PCR reaction  
-
===PROSITE===
+
==PROSITE==
* [[ProSA]] - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching  
* [[ProSA]] - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching  
-
===Protein binding sites===
+
==Protein binding sites==
* [[ConsInspector]] - A tool for the prediction of protein binding sites in nucleic acids  
* [[ConsInspector]] - A tool for the prediction of protein binding sites in nucleic acids  
-
===Protein docking===
+
==Protein docking==
* [[ZDOCK]] - Protein-protein complex structure prediction software  
* [[ZDOCK]] - Protein-protein complex structure prediction software  
-
===Protein domains===
+
==Protein domains==
* [[DomainFinder]] - DomainFinder 1.0  DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins
* [[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  
* [[ProSA]] - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching  
-
===Protein families===
+
==Protein families==
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER  
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER  
-
===Protein interaction===
+
==Protein interaction==
* [[ZDOCK]] - Protein-protein complex structure prediction software  
* [[ZDOCK]] - Protein-protein complex structure prediction software  
-
===Protein modelling===
+
==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  
* [[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===
+
==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.
* [[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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* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
-
===Protein structure prediction===
+
==Protein structure prediction==
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
-
===Protein/DNA/RNA family clustering===
+
==Protein/DNA/RNA family clustering==
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.  
-
===PubMed===
+
==PubMed==
* [[BioMail]] - automate searching for recent scientific papers in the PubMed Medline database  
* [[BioMail]] - automate searching for recent scientific papers in the PubMed Medline database  
-
===Python===
+
==Python==
* [[Biopython]] - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
* [[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.  
* [[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===
+
==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.  
* [[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===
+
==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.  
* [[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===
+
==Regular expressions==
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.  
* [[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===
+
==Regulatory sequence analysis==
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.  
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.  
-
===Rendered animations===
+
==Rendered animations==
* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems  
* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems  
-
===RNA===
+
==RNA==
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
Line 708: Line 708:
* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison  
* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison  
-
===RNA folding===
+
==RNA folding==
* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison  
* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison  
-
===RNA gene finder===
+
==RNA gene finder==
* [[NCRNASCAN]] - a structural RNA genefinder  
* [[NCRNASCAN]] - a structural RNA genefinder  
-
===RNA motif===
+
==RNA motif==
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher  
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher  
-
===RNA pseudoknots===
+
==RNA pseudoknots==
* [[PKNOTS]] - RNA pseudoknot prediction  
* [[PKNOTS]] - RNA pseudoknot prediction  
-
===RNA secondary structure===
+
==RNA secondary structure==
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
* [[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.  
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.  
-
===SCF===
+
==SCF==
* [[phrap]] - a program for assembling shotgun DNA sequence data
* [[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.  
* [[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===
+
==Secondary structure==
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
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* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings  
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings  
-
===SEPON===
+
==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  
* [[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===
+
==Sequences==
* [[ARB]] - Microbiologist's sequence database tool
* [[ARB]] - Microbiologist's sequence database tool
Line 786: Line 786:
* [[WU-Blast]] - Washington U. [[BLAST]]  
* [[WU-Blast]] - Washington U. [[BLAST]]  
-
===Sequence alignment===
+
==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
* [[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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* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms  
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms  
-
===Sequence analysis===
+
==Sequence analysis==
* [[ARB]] - Microbiologist's sequence database tool
* [[ARB]] - Microbiologist's sequence database tool
Line 823: Line 823:
* [[WU-Blast]] - Washington U. [[BLAST]]  
* [[WU-Blast]] - Washington U. [[BLAST]]  
-
===Sequence comparisons===
+
==Sequence comparisons==
* [[DBWatcher]] - DBWatcher is a program handling periodic [[BLAST]] searches to find similarities to your own sequences.  
* [[DBWatcher]] - DBWatcher is a program handling periodic [[BLAST]] searches to find similarities to your own sequences.  
-
===Sequence conversion===
+
==Sequence conversion==
* [[readseq]] - Reads and writes nucleic/protein sequences in various format  
* [[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  
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format  
-
===Sequence databases===
+
==Sequence databases==
* [[ARB]] - Microbiologist's sequence database tool  
* [[ARB]] - Microbiologist's sequence database tool  
-
===Sequence editor===
+
==Sequence editor==
* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
* [[SeqPup]] - SeqPup biological sequence editor and analysis program  
* [[SeqPup]] - SeqPup biological sequence editor and analysis program  
-
===Sequence finishing===
+
==Sequence finishing==
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies  
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies  
-
===Sequence patterns===
+
==Sequence patterns==
* [[Pratt]] - a pattern discovery tool  
* [[Pratt]] - a pattern discovery tool  
-
===Sequence similarity===
+
==Sequence similarity==
* [[BLAST]] - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases  
* [[BLAST]] - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases  
-
===Sequence utilities===
+
==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  
* [[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===
+
==Sequencing==
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
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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.  
* [[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===
+
==Smith-Waterman==
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
* [[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.  
* [[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===
+
==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  
* [[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===
+
==Statistical mechanics==
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.  
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.  
-
===Steric size calculation===
+
==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  
* [[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===
+
==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  
* [[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===
+
==Structural biology==
* [[DINO]] - a realtime 3D visualization program for structural biology data.  
* [[DINO]] - a realtime 3D visualization program for structural biology data.  
-
===Structure===
+
==Structure==
* [[Abacus]] - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of 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.
Line 906: Line 906:
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings  
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings  
-
===Structure analysis===
+
==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
* [[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  
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis  
-
===Structure prediction===
+
==Structure prediction==
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
-
===Substitution===
+
==Substitution==
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
* [[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.  
* [[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===
+
==Substitution rates==
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood  
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood  
-
===SwissProt===
+
==SwissProt==
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format  
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format  
-
===Tcl/Tk===
+
==Tcl/Tk==
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language  
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language  
-
===Thermodynamics===
+
==Thermodynamics==
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
* [[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  
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex  
-
===Threading===
+
==Threading==
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
-
===Trace===
+
==Trace==
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
Line 950: Line 950:
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments  
-
===Trace chromatogram===
+
==Trace chromatogram==
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.  
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.  
-
===Trace files===
+
==Trace files==
* [[phrap]] - a program for assembling shotgun DNA sequence data
* [[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.
* [[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===
+
==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  
* [[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===
+
==Transcription factors==
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences  
* [[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.  
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.  
-
===Trees===
+
==Trees==
* [[ATV]] - a phylogenetic tree display tool
* [[ATV]] - a phylogenetic tree display tool
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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.   
* [[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===
+
==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.  
* [[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===
+
==Tree viewers==
* [[ATV]] - a phylogenetic tree display tool
* [[ATV]] - a phylogenetic tree display tool
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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.   
* [[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===
+
==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.  
* [[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===
+
==Visualization==
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics  
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics  
Line 1,011: Line 1,011:
* [[VMD]] - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting  
* [[VMD]] - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting  
-
===VMD===
+
==VMD==
* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.   
* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.   
-
===Web robots===
+
==Web robots==
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.  
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.  
-
===Workflow===
+
==Workflow==
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.

Revision as of 00:07, 17 July 2007

Contents

3D structure visualization

Applied Biosystems (ABI)

Affine gap

Alignment

Amplification

Analytical ultracentrifugation

Aneda

Assembly

Base calling

Bayesian methods

BioCoRE

BLAST

C. elegans

CASP

Chemical kinetics

Chemical structures

Chromatogram

Code generators

Comparative analysis

Comparative genetics

Composition

Correlation

Crystallography

Data analysis

Data flow

Data mining

Databases

Database interface

Database searching

Database segmentation

Denaturation

Dictionaries

Distance correlations

DNA sequence viewer

DNA sequencing

DNA structure

Drawing

Duplications

Electron density maps

EMBL

EMBOSS

EST

EST clustering similarity alignment

EVA

Evolution

Exons

Extensions

File conversion

Finite elements

Fold recognition

Format converters

GenBank entry visualization

Gene duplications

Gene expression

Gene finding

Gene regulation

Genetic distances

Genome annotation

Genome development libraries

Genome rearrangement

Genome retrieval

Genomic database system

Genomics

GFF

Global fitting

Graph theory

grep

Group-specific primers

Hidden Markov Models

Homologous genes

Inference

Java

Libraries

Maximum likelihood

MCMC

Medline

Melting temperature

Microarray analysis

Modeling

Molecular dynamics

Molecular editors

Molecular graphics

Molecular mechanics

Molecular modeling

Molecular simulations

Molecular structure analysis

Molecular visualization

Molecular weight

Monte Carlo

Motifs

MPI

Multiple

Multiple alignment editors

Multiple genome alignment

Multiple protein structure visualization

Multiple sequence alignment

Multiple sequence alignment drawing

MySQL

NAMD

Neural networks

NMR

Nucleic acids

Oligonucleotides

Online searching

Online tools

Parallel

Patterns

PCR

PDB

Perl

Phase

Phenotype analysis

Phylogenetics

Phylogenetic trees

Phylogenetic tree reconstruction

Phylogenomics

PostScript

POV-Ray

Prediction

Primers

PROSITE

Protein binding sites

Protein docking

Protein domains

Protein families

Protein interaction

Protein modelling

Protein structure

Protein structure prediction

Protein/DNA/RNA family clustering

PubMed

Python

Real-time visualization

Reannotation

Regular expressions

Regulatory sequence analysis

Rendered animations

RNA

RNA folding

RNA gene finder

RNA motif

RNA pseudoknots

RNA secondary structure

SCF

Secondary structure

SEPON

Sequences

Sequence alignment

Sequence analysis

Sequence comparisons

Sequence conversion

Sequence databases

Sequence editor

Sequence finishing

Sequence patterns

Sequence similarity

Sequence utilities

Sequencing

Smith-Waterman

Solid Angle calculation

Statistical mechanics

Steric size calculation

Structural alignments

Structural biology

Structure

Structure analysis

Structure prediction

Substitution

Substitution rates

SwissProt

Tcl/Tk

Thermodynamics

Threading

Trace

Trace chromatogram

Trace files

Trajectory analysis

Transcription factors

Trees

Tree of life

Tree viewers

tRNA searching

Visualization

VMD

Web robots

Workflow

Personal tools
Namespaces
Variants
Actions
wiki navigation
Toolbox