Software

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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.  
* [[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.  
-
===ABI===
+
===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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* [[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
* [[xsact]] - EST clustering tool  
* [[xsact]] - EST clustering tool  
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===Alignment editor===
 
-
 
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* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
 
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* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
 
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* [[Jalview]] - Jalview - a java multiple alignment editor
 
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* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
 
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* [[seaview]] - SeaView is a graphical multiple sequence alignment editor 
 
-
 
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===Alignment viewer===
 
-
 
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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.
 
===Amplification===
===Amplification===
* [[Amplicon]] - Program for designing group-specific PCR primer sets  
* [[Amplicon]] - Program for designing group-specific PCR primer sets  
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-
===Analysis===
 
-
 
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* [[ARB]] - Microbiologist's sequence database tool
 
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* [[BioJava]] - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
 
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* [[Biopython]] - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
 
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* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
 
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* [[Blast]] - BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
 
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
 
-
* [[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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* [[clustalw]] - The famous ClustalW multiple alignment program
 
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* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
 
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* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
 
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* [[DNA-GUI]] - DNA Graphical User Interface
 
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* [[EMBOSS]] - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
 
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* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
 
-
* [[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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* [[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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* [[NCRNASCAN]] - a structural RNA genefinder
 
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* [[PatScan]] - PatScan is a  pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
 
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* [[PKNOTS]] - RNA pseudoknot prediction
 
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* [[Pratt]] - a pattern discovery tool
 
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* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
 
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* [[readseq]] - Reads and writes nucleic/protein sequences in various format
 
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* [[SEALS]] - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
 
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* [[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.
 
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* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
 
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* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.
 
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* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
 
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* [[TREE-PUZZLE]] - Maximum likelihood analysis for nucleotide, amino acid, and two-state data
 
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* [[tRNAscan-SE]] - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
 
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
 
-
* [[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
 
-
* [[WU-Blast]] - Washington U. [[BLAST]]
 
===Analytical ultracentrifugation===
===Analytical ultracentrifugation===
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* [[phrap]] - a program for assembling shotgun DNA sequence data
* [[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.  
* [[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.  
-
 
-
===Automated phylogenetic analysis===
 
-
 
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* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
 
===Base calling===
===Base calling===
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* [[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.  
-
 
-
===Bayesian===
 
-
 
-
* [[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.
 
===Bayesian methods===
===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.
===BioCoRE===
===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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-
===Bioinformatics===
 
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* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
 
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===Biological macromolecule===
 
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* [[Garlic]] - a free molecular visualization program
 
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===biological sequence editor===
 
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* [[SeqPup]] - SeqPup biological sequence editor and analysis program
 
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===Biosequence===
 
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* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
 
===BLAST===
===BLAST===
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* [[MSPcrunch]] - a BLAST enhancement filter
* [[MSPcrunch]] - a BLAST enhancement filter
* [[WU-Blast]] - Washington U. [[BLAST]]  
* [[WU-Blast]] - Washington U. [[BLAST]]  
-
 
-
===BLAST filter===
 
-
 
-
* [[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.
 
-
* [[MSPcrunch]] - a [[BLAST]] enhancement filter
 
-
 
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===Bond and atom rendering===
 
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* [[Spock]] - a full-featured molecular graphics program
 
===C. elegans===
===C. elegans===
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* [[Angler]] - A Browser of C.elegans Embryo Development In Time and Space  
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* [[Angler]] - A Browser of ''C. elegans'' Embryo Development In Time and Space  
-
 
+
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===CAFASP===
+
-
 
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
===CASP===
===CASP===
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results  
+
* [[LIBELLULA]] - A neural network based web server to evaluate fold recognition results  
===Chemical kinetics===
===Chemical kinetics===
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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.  
-
===Database===
+
===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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* [[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.   
-
===Dictionary===
+
===Dictionaries===
* [[Leksbot]] - an explanatory dictionary of botanic and biological terms  
* [[Leksbot]] - an explanatory dictionary of botanic and biological terms  
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* [[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 melting===
 
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* [[MeltSim]] - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake. 
 
===DNA sequence viewer===
===DNA sequence viewer===
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* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
* [[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.
* [[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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===Duplications.===
 
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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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* [[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.  
-
===Extension===
+
===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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* [[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  
-
===Finite element===
+
===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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* [[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  
-
===Format converter===
+
===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  
-
===GenBank Entry Visualization===
+
===GenBank entry visualization===
* [[GeneView II]] - Interactive GenBank Entry Visualization  
* [[GeneView II]] - Interactive GenBank Entry Visualization  
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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  
-
===Genome development library===
+
===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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* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis  
* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis  
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===Genomes===
 
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* [[GenomePixelizer]] - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
 
===Genomic database system===
===Genomic database system===
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* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.  
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.  
-
===Group-specific===
+
===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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* [[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.  
-
===Library===
+
===Libraries===
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
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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 editor===
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===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.  
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* [[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  
-
===Motif===
+
===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.
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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 editor===
+
===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 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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* [[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.  
-
===Pattern===
+
===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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* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript  
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript  
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===POV-Ray scenes===
+
===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  
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* [[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 database===
+
===Sequence databases===
* [[ARB]] - Microbiologist's sequence database tool  
* [[ARB]] - Microbiologist's sequence database tool  
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* [[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  
-
 
-
===Stuctures===
 
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* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
 
===Substitution===
===Substitution===
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* [[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. <h3><a name="trajectory analysis">trajectory analysis===
+
* [[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  
* [[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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* [[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 viewer===
+
===Tree viewers===
* [[ATV]] - a phylogenetic tree display tool
* [[ATV]] - a phylogenetic tree display tool
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===Workflow===
===Workflow===
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* [[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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===xchange biological data===
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* [[OmniGene]] - Standardizing Biological Data Interchange Through Web Services Technology
+

Revision as of 00:23, 17 May 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