Software

From Bioinformatics.Org Wiki

(Difference between revisions)
Jump to: navigation, search
m (List of Linux programs moved to Software: More general)
(Removed software; left categories)
Line 1: Line 1:
-
==3D structure visualization==
+
==0-9==
-
* [[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.
+
* [[3D structure visualization]]
-
==Applied Biosystems (ABI)==
+
==A-C==
-
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
+
* [[Applied Biosystems (ABI)]]
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
* [[Affine gap]]
-
* [[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.
+
* [[Alignment]]
-
* [[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. 
+
* [[Amplification]]
-
==Affine gap==
+
* [[Analytical ultracentrifugation]]
-
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
+
* [[Aneda]]
-
==Alignment==
+
* [[Assembly]]
-
* [[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.
+
* [[Base calling]]
-
* [[Chimera]] - Excellent molecular graphics package with  support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven  analysis, multiple sequence alignment analysis, multiple model analysis, dockin
+
-
* [[clustalw]] - The famous ClustalW multiple alignment program
+
-
* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
+
-
* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
+
-
* [[Deep View Swiss-PdbViewer]] - Swiss-PdbViewer is an application that provides a user          friendly interface allowing to analyse several proteins at the same time
+
-
* [[DIALIGN]] - DIALIGN is an alignment program that relies on comparison of whole segments of the sequences instead of comparison of single residue
+
-
* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
+
-
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
+
-
* [[Jalview]] - Jalview - a java multiple alignment editor
+
-
* [[Mauve]] - Mauve is a multiple genome alignment and visualization package that  considers large-scale rearrangements in addition to nucleotide substitution and indels.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
+
-
* [[PhyloDraw]] -  PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
+
-
* [[SAM equence Alignment and Modeling Syste]] - a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
-
* [[ShadyBox]] - ShadyBox The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
* [[xsact]] - EST clustering tool
+
-
==Amplification==
+
* [[Bayesian methods]]
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
* [[BioCoRE]]
-
==Analytical ultracentrifugation==
+
* [[BLAST]]
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
* [[C. elegans]]
-
==Aneda==
+
* [[CASP]]
-
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
+
* [[Chemical kinetics]]
-
==Assembly==
+
* [[Chemical structures]]
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
* [[Chromatogram]]
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[Staden Package]] - This is a free to academics (charge for commercial users) package including sequence assemble, trace viewing/editing and sequence analysis tools. It also includes a GUI to the free EMBOSS suite.
+
-
==Base calling==
+
* [[Code generators]]
-
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
+
* [[Comparative 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.
+
-
==Bayesian methods==
+
* [[Comparative genetics]]
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
* [[Composition]]
-
* [[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==
+
* [[Correlation]]
-
* [[NAMD]] - NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. 
+
* [[Crystallography]]
-
==BLAST==
+
==D-F==
-
* [[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.
+
* [[Data analysis]]
-
* [[DBWatcher]] - DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.
+
-
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
+
-
* [[MSPcrunch]] - a BLAST enhancement filter
+
-
* [[WU-Blast]] - Washington U. [[BLAST]]  
+
-
==C. elegans==
+
* [[Data flow]]
-
* [[Angler]] - A Browser of ''C. elegans'' Embryo Development In Time and Space
+
* [[Data mining]]
-
==CASP==
+
* [[Databases]]
-
* [[LIBELLULA]] - A neural network based web server to evaluate fold recognition results
+
* [[Database interface]]
-
==Chemical kinetics==
+
* [[Database searching]]
-
* [[Kintecus]] -  Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
+
* [[Database segmentation]]
-
==Chemical structures==
+
* [[Denaturation]]
-
* [[MOPAC7]] - a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
+
* [[Dictionaries]]
-
==Chromatogram==
+
* [[Distance correlations]]
-
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
+
* [[DNA sequence viewer]]
-
* [[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.
+
-
==Code generators==
+
* [[DNA sequencing]]
-
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
+
* [[DNA structure]]
-
==Comparative analysis==
+
* [[Drawing]]
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
* [[Duplications]]
-
==Comparative genetics==
+
* [[Electron density maps]]
-
* [[GenomePixelizer]] - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
+
* [[EMBL]]
-
==Composition==
+
* [[EMBOSS]]
-
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
+
* [[EST]]
-
==Correlation==
+
* [[EST clustering similarity alignment]]
-
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
+
* [[EVA]]
-
* [[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.
+
-
==Crystallography==
+
* [[Evolution]]
-
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
+
* [[Exons]]
-
==Data analysis==
+
* [[Extensions]]
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
* [[File conversion]]
-
==Data flow==
+
* [[Finite elements]]
-
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
+
* [[Fold recognition]]
-
==Data mining==
+
* [[Format converters]]
-
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
+
==G-I==
-
* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.
+
-
==Databases==
+
* [[GenBank entry visualization]]
-
* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project
+
* [[Gene duplications]]
-
* [[ARB]] - Microbiologist's sequence database tool
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[HMMER]] - Profile hidden Markov models for biological sequence analysis
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
+
-
==Database interface==
+
* [[Gene expression]]
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
* [[Gene finding]]
-
==Database searching==
+
* [[Gene regulation]]
-
* [[HMMER]] - Profile hidden Markov models for biological sequence analysis 
+
* [[Genetic distances]]
-
==Database segmentation==
+
* [[Genome annotation]]
-
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
+
* [[Genome development libraries]]
-
==Denaturation==
+
* [[Genome rearrangement]]
-
* [[MeltSim]] - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake. 
+
* [[Genome retrieval]]
-
==Dictionaries==
+
* [[Genomic database system]]
-
* [[Leksbot]] - an explanatory dictionary of botanic and biological terms
+
* [[Genomics]]
-
==Distance correlations==
+
* [[GFF]]
-
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
+
* [[Global fitting]]
-
==DNA sequence viewer==
+
* [[Graph theory]]
-
* [[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.
+
* [[grep]]
-
==DNA sequencing==
+
* [[Group-specific primers]]
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
* [[Hidden Markov Models]]
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[phred]] - Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
+
-
==DNA structure==
+
* [[Homologous genes]]
-
* [[Garlic]] - a free molecular visualization program
+
* [[Inference]]
-
==Drawing==
+
==J-L==
-
* [[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
+
* [[Java]]
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
==Duplications==
+
* [[Libraries]]
-
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
+
==M-O==
-
* [[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.
+
-
==Electron density maps==
+
* [[Maximum likelihood]]
-
* [[Deep View Swiss-PdbViewer]] - Swiss-PdbViewer is an application that provides a user          friendly interface allowing to analyse several proteins at the same time
+
* [[MCMC]]
-
==EMBL==
+
* [[Medline]]
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
* [[Melting temperature]]
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
+
-
* [[Staden Package]] - This is a free to academics (charge for commercial users) package including sequence assemble, trace viewing/editing and sequence analysis tools. It also includes a GUI to the free EMBOSS suite.
+
-
==EMBOSS==
+
* [[Microarray analysis]]
-
* [[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.
+
* [[Modeling]]
-
==EST==
+
* [[Molecular dynamics]]
-
* [[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
+
* [[Molecular editors]]
-
* [[xsact]] - EST clustering tool
+
-
==EST clustering similarity alignment==
+
* [[Molecular graphics]]
-
* [[xsact]] - EST clustering tool
+
* [[Molecular mechanics]]
-
==EVA==
+
* [[Molecular modeling]]
-
* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis
+
* [[Molecular simulations]]
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
==Evolution==
+
* [[Molecular structure analysis]]
-
* [[GenomePixelizer]] - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
+
* [[Molecular visualization]]
-
* [[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.
+
-
==Exons==
+
* [[Molecular weight]]
-
* [[Abacus]] - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
+
* [[Monte Carlo]]
-
==Extensions==
+
* [[Motifs]]
-
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
+
* [[MPI]]
-
==File conversion==
+
* [[Multiple]]
-
* [[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
+
* [[Multiple alignment editors]]
-
==Finite elements==
+
* [[Multiple genome alignment]]
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
* [[Multiple protein structure visualization]]
-
==Fold recognition==
+
* [[Multiple sequence alignment]]
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
* [[Multiple sequence alignment drawing]]
-
==Format converters==
+
* [[MySQL]]
-
* [[Babel]] - a program designed to interconvert a number of  file formats currently used in molecular modeling
+
* [[NAMD]]
-
==GenBank entry visualization==
+
* [[Neural networks]]
-
* [[GeneView II]] - Interactive GenBank Entry Visualization
+
* [[NMR]]
-
==Gene duplications==
+
* [[Nucleic acids]]
-
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
+
* [[Oligonucleotides]]
-
==Gene expression==
+
* [[Online searching]]
-
* [[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.
+
* [[Online tools]]
-
* [[SEPON]] - SEPON designs gene-specific oligonucleotides for microarray experiments and is able to use EST input from organisms in which the genome is not annotated for genes. SEPON implements a novel algorithm for reducing cross-hybridization by utilizing thermodyna
+
-
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
+
-
==Gene finding==
+
==P-R==
-
* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd
+
* [[Parallel]]
-
* [[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.
+
-
==Gene regulation==
+
* [[Patterns]]
-
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
+
* [[PCR]]
-
==Genetic distances==
+
* [[PDB]]
-
* [[Populations]] - Population genetic software (individuals or populations distances, phylogenetic trees)
+
* [[Perl]]
-
==Genome annotation==
+
* [[Phase]]
-
* [[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.
+
* [[Phenotype analysis]]
-
* [[Ensembl]] - software system which produces and maintains automatic annotation on eukaryoticgenomes
+
-
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
+
-
* [[On-line Genome Annotations]] - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features
+
-
==Genome development libraries==
+
* [[Phylogenetics]]
-
* [[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.
+
* [[Phylogenetic trees]]
-
==Genome rearrangement==
+
* [[Phylogenetic tree reconstruction]]
-
* [[GRIL]] - GRIL automates the process of identifying large-scale genome inversions and rearrangements
+
* [[Phylogenomics]]
-
==Genome retrieval==
+
* [[PostScript]]
-
* [[GRS]] - A Graphic Tool for Genome Retrieval and Segment Analysis
+
* [[POV-Ray]]
-
==Genomic database system==
+
* [[Prediction]]
-
* [[Acedb]] - Acedb is a genome database system originally developed for the C.elegans genome project
+
* [[Primers]]
-
==Genomics==
+
* [[PROSITE]]
-
* [[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
+
* [[Protein binding sites]]
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
==GFF==
+
* [[Protein docking]]
-
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
+
* [[Protein domains]]
-
==Global fitting==
+
* [[Protein families]]
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
* [[Protein interaction]]
-
==Graph theory==
+
* [[Protein modelling]]
-
* [[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.
+
* [[Protein structure]]
-
==grep==
+
* [[Protein structure prediction]]
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
* [[Protein/DNA/RNA family clustering]]
-
==Group-specific primers==
+
* [[PubMed]]
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
* [[Python]]
-
==Hidden Markov Models==
+
* [[Real-time visualization]]
-
* [[HMMER]] - Profile hidden Markov models for biological sequence analysis
+
* [[Reannotation]]
-
* [[SAM equence Alignment and Modeling Syste]] - a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
+
-
* [[VEIL]] - A hidden Markov model for finding genes in vertebrate DNA\ufffd
+
-
==Homologous genes==
+
* [[Regular expressions]]
-
* [[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.
+
* [[Regulatory sequence analysis]]
-
==Inference==
+
* [[Rendered animations]]
-
* [[MOLPHY]] - A Computer Program Package for Molecular Phylogenetics including ProtML
+
* [[RNA]]
-
* [[PHASE]] - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
+
-
==Java==
+
* [[RNA folding]]
-
* [[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.
+
* [[RNA gene finder]]
-
* [[BioJava]] - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
+
-
* [[MAExplorer]] - The Microarray Explorer (MAExplorer) is a Java-based data-mining facility for microarray databases run as a stand-alone program. It includes graphics, statistics, clustering, reports, data filtering.
+
-
==Libraries==
+
* [[RNA motif]]
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
* [[RNA pseudoknots]]
-
* [[libGenome]] - A cross platform C++ development library to manipulate DNA and protein sequences.  It can read and write sequence and annotation data in several file formats.
+
-
==Maximum likelihood==
+
* [[RNA secondary structure]]
-
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
+
==S-U==
-
* [[MOLPHY]] - A Computer Program Package for Molecular Phylogenetics including ProtML
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[TREE-PUZZLE]] - Maximum likelihood analysis for nucleotide, amino acid, and two-state data
+
-
==MCMC==
+
* [[Secondary structure]]
-
* [[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.
+
* [[Sequences]]
-
==Medline==
+
* [[Sequence alignment]]
-
* [[BioMail]] - automate searching for recent scientific papers in the PubMed Medline database
+
* [[Sequence analysis]]
-
==Melting temperature==
+
* [[Sequence comparisons]]
-
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
+
* [[Sequence conversion]]
-
* [[MeltSim]] - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake. 
+
-
==Microarray analysis==
+
* [[Sequence databases]]
-
* [[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.
+
* [[Sequence editor]]
-
* [[SEPON]] - SEPON designs gene-specific oligonucleotides for microarray experiments and is able to use EST input from organisms in which the genome is not annotated for genes. SEPON implements a novel algorithm for reducing cross-hybridization by utilizing thermodyna
+
-
* [[Teiresias-based Gene expression analysis]] - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.
+
-
==Modeling==
+
* [[Sequence finishing]]
-
* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.
+
* [[Sequence patterns]]
-
* [[Kintecus]] -  Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
+
-
* [[MMTK-2.2]] - molecular modeling tool-kit 2.2
+
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
* [[WHAT IF]] - WHAT  IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc
+
-
==Molecular dynamics==
+
* [[Sequence similarity]]
-
* [[Gromacs]] - The World' s fastest Molecular Dynamics - and it' s gpl
+
* [[Sequence utilities]]
-
* [[MMTK-2.2]] - molecular modeling tool-kit 2.2
+
-
* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems
+
-
==Molecular editors==
+
* [[Sequencing]]
-
* [[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.
+
* [[Smith-Waterman]]
-
==Molecular graphics==
+
* [[Solid Angle calculation]]
-
* [[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
+
* [[Statistical mechanics]]
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
* [[Spock]] - a full-featured molecular graphics program
+
-
==Molecular mechanics==
+
* [[Steric size calculation]]
-
* [[AMMP]] - a modern full-featured molecular mechanics, dynamics and modeling program.
+
* [[Structural alignments]]
-
==Molecular modeling==
+
* [[Structural biology]]
-
* [[Babel]] - a program designed to interconvert a number of  file formats currently used in molecular modeling
+
* [[Structure]]
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
* [[WHAT IF]] - WHAT  IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc
+
-
==Molecular simulations==
+
* [[Structure analysis]]
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
* [[Structure prediction]]
-
==Molecular structure analysis==
+
* [[Substitution]]
-
* [[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
+
* [[Substitution rates]]
-
==Molecular visualization==
+
* [[SwissProt]]
-
* [[Garlic]] - a free molecular visualization program
+
* [[Tcl/Tk]]
-
* [[rasmol]] - RasMol is a free program which displays molecular structure.
+
-
* [[VEGA]] -  VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D struct
+
-
* [[VMD]] - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
+
-
==Molecular weight==
+
* [[Thermodynamics]]
-
* [[XMolCalc]] - a small utility that allows you to calculate a molecular weight
+
* [[Threading]]
-
==Monte Carlo==
+
* [[Trace]]
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
* [[Trace chromatogram]]
-
==Motifs==
+
* [[Trace files]]
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
* [[Trajectory analysis]]
-
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher
+
-
==MPI==
+
* [[Transcription factors]]
-
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
+
* [[Trees]]
-
==Multiple==
+
* [[Tree of life]]
-
* [[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
+
* [[Tree viewers]]
-
* [[clustalw]] - The famous ClustalW multiple alignment program
+
-
* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
+
-
* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[Jalview]] - Jalview - a java multiple alignment editor
+
-
* [[Mauve]] - Mauve is a multiple genome alignment and visualization package that  considers large-scale rearrangements in addition to nucleotide substitution and indels.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
==Multiple alignment editors==
+
* [[tRNA searching]]
-
* [[DCSE]] - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
+
==V-Z==
-
* [[Jalview]] - Jalview - a java multiple alignment editor
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
==Multiple genome alignment==
+
* [[Visualization]]
-
* [[Mauve]] - Mauve is a multiple genome alignment and visualization package that  considers large-scale rearrangements in addition to nucleotide substitution and indels.
+
* [[VMD]]
-
==Multiple protein structure visualization==
+
* [[Web robots]]
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
* [[Workflow]]
-
 
+
-
==Multiple sequence alignment==
+
-
 
+
-
* [[Chimera]] - Excellent molecular graphics package with  support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven  analysis, multiple sequence alignment analysis, multiple model analysis, dockin
+
-
* [[clustalw]] - The famous ClustalW multiple alignment program
+
-
* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
 
+
-
==Multiple sequence alignment drawing==
+
-
 
+
-
* [[ShadyBox]] - The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
 
+
-
==MySQL==
+
-
 
+
-
* [[Ensembl]] - software system which produces and maintains automatic annotation on eukaryoticgenomes
+
-
 
+
-
==NAMD==
+
-
 
+
-
* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
+
-
 
+
-
==Neural networks==
+
-
 
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
+
-
 
+
-
==NMR==
+
-
 
+
-
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
+
-
 
+
-
==Nucleic acids==
+
-
 
+
-
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
+
-
 
+
-
==Oligonucleotides==
+
-
 
+
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
-
* [[SEPON]] - SEPON designs gene-specific oligonucleotides for microarray experiments and is able to use EST input from organisms in which the genome is not annotated for genes. SEPON implements a novel algorithm for reducing cross-hybridization by utilizing thermodyna
+
-
 
+
-
==Online searching==
+
-
 
+
-
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
+
-
 
+
-
==Online tools==
+
-
 
+
-
* [[On-line Genome Annotations]] - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features
+
-
 
+
-
==Parallel==
+
-
 
+
-
* [[mpiBLAST]] - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
+
-
 
+
-
==Patterns==
+
-
 
+
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[PatScan]] - PatScan is a  pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
+
-
* [[Pratt]] - a pattern discovery tool
+
-
 
+
-
==PCR==
+
-
 
+
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
-
 
+
-
==PDB==
+
-
 
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[MMTK-2.2]] - molecular modeling tool-kit 2.2
+
-
 
+
-
==Perl==
+
-
 
+
-
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
+
-
 
+
-
==Phase==
+
-
 
+
-
* [[PHASE]] - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
+
-
 
+
-
==Phenotype analysis==
+
-
 
+
-
* [[Teiresias-based Association Discovery]] - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
+
-
 
+
-
==Phylogenetics==
+
-
 
+
-
* [[ATV]] - a phylogenetic tree display tool
+
-
* [[Clann]] - Clann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree  analysis (which are used as optimality criteria) and allows exhaustive and  heuristic searches of tree-space to find the best supert
+
-
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[MOLPHY]] - A Computer Program Package for Molecular Phylogenetics including ProtML
+
-
* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[Paup]] - Software package for inference of evolutionary trees
+
-
* [[PHASE]] - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
+
-
* [[PHYLIP]] - PHYLIP is a free package of programs for inferring phylogenies.
+
-
* [[PhyloDraw]] -  PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
+
-
* [[PhyloGrapher]] - PhyloGrapher is a program designed to visualize and study evolutional relationship between families of homologous genes or proteins. PhyloGrapher is a drawing tool that generates custom graphs out of the given set of genes based on distance matrix file.
+
-
* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
* [[unrooted]] - Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches. 
+
-
 
+
-
==Phylogenetic trees==
+
-
 
+
-
* [[ATV]] - a phylogenetic tree display tool
+
-
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
+
-
* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[Paup]] - Software package for inference of evolutionary trees
+
-
* [[PHYLIP]] - PHYLIP is a free package of programs for inferring phylogenies.
+
-
* [[PhyloDraw]] -  PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
+
-
* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
* [[unrooted]] - Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches. 
+
-
 
+
-
==Phylogenetic tree reconstruction==
+
-
 
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
 
+
-
==Phylogenomics==
+
-
 
+
-
* [[Clann]] - Clann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree  analysis (which are used as optimality criteria) and allows exhaustive and  heuristic searches of tree-space to find the best supert
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
 
+
-
==PostScript==
+
-
 
+
-
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
+
-
 
+
-
==POV-Ray==
+
-
 
+
-
* [[Deep View Swiss-PdbViewer]] - Swiss-PdbViewer is an application that provides a user          friendly interface allowing to analyse several proteins at the same time
+
-
 
+
-
==Prediction==
+
-
 
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[ConsInspector]] - A tool for the prediction of protein binding sites in nucleic acids
+
-
* [[geneid]] -  Gene prediction tool, it can also introduce homology and annotation evidences and produce a reannotation of a genomic sequence. A pthreads parallel version also available.
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
-
==Primers==
+
-
 
+
-
* [[Amplicon]] - Program for designing group-specific PCR primer sets
+
-
* [[primer]] - a program for picking primers for PCR reaction
+
-
 
+
-
==PROSITE==
+
-
 
+
-
* [[ProSA]] - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching
+
-
 
+
-
==Protein binding sites==
+
-
 
+
-
* [[ConsInspector]] - A tool for the prediction of protein binding sites in nucleic acids
+
-
 
+
-
==Protein docking==
+
-
 
+
-
* [[ZDOCK]] - Protein-protein complex structure prediction software
+
-
 
+
-
==Protein domains==
+
-
 
+
-
* [[DomainFinder]] - DomainFinder 1.0  DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins
+
-
* [[ProSA]] - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching
+
-
 
+
-
==Protein families==
+
-
 
+
-
* [[GEANFAMMER]] - GEnome ANalysis and Protein FAMily MakER
+
-
 
+
-
==Protein interaction==
+
-
 
+
-
* [[ZDOCK]] - Protein-protein complex structure prediction software
+
-
 
+
-
==Protein modelling==
+
-
 
+
-
* [[BRAGI]] - BRAGI is a interactive protein modelling and display program. It was developed for the special purpose to modell unknown proteins from the structure of  a known one
+
-
 
+
-
==Protein structure==
+
-
 
+
-
* [[Abacus]] - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
* [[MODELLER]] - a program for homology protein structure modelling by satisfaction of spatial restraints.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
 
+
-
==Protein structure prediction==
+
-
 
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
-
==Protein/DNA/RNA family clustering==
+
-
 
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
 
+
-
==PubMed==
+
-
 
+
-
* [[BioMail]] - automate searching for recent scientific papers in the PubMed Medline database
+
-
 
+
-
==Python==
+
-
 
+
-
* [[Biopython]] - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
 
+
-
==Real-time visualization==
+
-
 
+
-
* [[PyMol]] - PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
+
-
 
+
-
==Reannotation==
+
-
 
+
-
* [[geneid]] -  Gene prediction tool, it can also introduce homology and annotation evidences and produce a reannotation of a genomic sequence. A pthreads parallel version also available.
+
-
 
+
-
==Regular expressions==
+
-
 
+
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
-
 
+
-
==Regulatory sequence analysis==
+
-
 
+
-
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
+
-
 
+
-
==Rendered animations==
+
-
 
+
-
* [[GDIS]] - a GTK based program for the display and manipulation of isolated molecules and periodic systems
+
-
 
+
-
==RNA==
+
-
 
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
+
-
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[NCRNASCAN]] - a structural RNA genefinder
+
-
* [[PHASE]] - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
+
-
* [[PKNOTS]] - RNA pseudoknot prediction
+
-
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
+
-
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher
+
-
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
+
-
* [[tRNAscan-SE]] - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
+
-
* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison
+
-
 
+
-
==RNA folding==
+
-
 
+
-
* [[Vienna RNA Package]] - RNA Secondary Structure Prediction and Comparison
+
-
 
+
-
==RNA gene finder==
+
-
 
+
-
* [[NCRNASCAN]] - a structural RNA genefinder
+
-
 
+
-
==RNA motif==
+
-
 
+
-
* [[RNABOB]] - RNABOB -- fast RNA motif/pattern searcher
+
-
 
+
-
==RNA pseudoknots==
+
-
 
+
-
* [[PKNOTS]] - RNA pseudoknot prediction
+
-
 
+
-
==RNA secondary structure==
+
-
 
+
-
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
+
-
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
+
-
 
+
-
==SCF==
+
-
 
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[phred]] - Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
+
-
 
+
-
==Secondary structure==
+
-
 
+
-
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
+
-
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
+
-
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
+
-
 
+
-
==SEPON==
+
-
 
+
-
* [[SEPON]] - SEPON designs gene-specific oligonucleotides for microarray experiments and is able to use EST input from organisms in which the genome is not annotated for genes. SEPON implements a novel algorithm for reducing cross-hybridization by utilizing thermodyna
+
-
 
+
-
==Sequences==
+
-
 
+
-
* [[ARB]] - Microbiologist's sequence database tool
+
-
* [[Artemis]] - a  DNA sequence viewer and annotation tool that allows  visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
+
-
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
+
-
* [[Biogrep]] - A grep that is optimized for biosequences.  Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
+
-
* [[BioJava]] - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
+
-
* [[Biopython]] - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
+
-
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
+
-
* [[BLAST]] - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
+
-
* [[Chimera]] - Excellent molecular graphics package with  support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven  analysis, multiple sequence alignment analysis, multiple model analysis, dockin
+
-
* [[clustalw]] - The famous ClustalW multiple alignment program
+
-
* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
+
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
-
* [[DBWatcher]] - DBWatcher is a program handling periodic [[BLAST]] searches to find similarities to your own sequences.
+
-
* [[DNA-GUI]] - DNA Graphical User Interface
+
-
* [[EMBOSS]] - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
+
-
* [[Genpak]] - a set of small utilities written in ANSI C to manipulate DNA sequences in a Unix fashion, fit for combining within shell and cgi scripts
+
-
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
+
-
* [[libGenome]] - A cross platform C++ development library to manipulate DNA and protein sequences.  It can read and write sequence and annotation data in several file formats.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
+
-
* [[NCRNASCAN]] - a structural RNA genefinder
+
-
* [[PatScan]] - PatScan is a  pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
+
-
* [[PhyloDraw]] -  PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
+
-
* [[PKNOTS]] - RNA pseudoknot prediction
+
-
* [[Pratt]] - a pattern discovery tool
+
-
* [[readseq]] - Reads and writes nucleic/protein sequences in various format
+
-
* [[SAM equence Alignment and Modeling Syste]] - a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
+
-
* [[SEALS]] - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
-
* [[SeqPup]] - SeqPup biological sequence editor and analysis program
+
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
+
-
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
+
-
* [[tRNAscan-SE]] - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
+
-
* [[WU-Blast]] - Washington U. [[BLAST]]
+
-
 
+
-
==Sequence alignment==
+
-
 
+
-
* [[Chimera]] - Excellent molecular graphics package with  support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven  analysis, multiple sequence alignment analysis, multiple model analysis, dockin
+
-
* [[clustalw]] - The famous ClustalW multiple alignment program
+
-
* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
+
-
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[Musca]] - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
+
-
* [[MUSCLE]] - Multiple sequence alignment. More accurate than T-Coffee, faster than  CLUSTALW.
+
-
* [[PhyloDraw]] -  PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
+
-
* [[SAM equence Alignment and Modeling Syste]] - a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
+
-
* [[seaview]] - SeaView is a graphical multiple sequence alignment editor
+
-
* [[ShadyBox.]] - ShadyBox. The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
+
-
 
+
-
==Sequence analysis==
+
-
 
+
-
* [[ARB]] - Microbiologist's sequence database tool
+
-
* [[BioJava]] - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
+
-
* [[Biopython]] - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
+
-
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
+
-
* [[BLAST]] - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
+
-
* [[clustalw]] - The famous ClustalW multiple alignment program
+
-
* [[clustalx]] - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
+
-
* [[DNA-GUI]] - DNA Graphical User Interface
+
-
* [[EMBOSS]] - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
+
-
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
+
-
* [[NCRNASCAN]] - a structural RNA genefinder
+
-
* [[PatScan]] - PatScan is a  pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
+
-
* [[PKNOTS]] - RNA pseudoknot prediction
+
-
* [[Pratt]] - a pattern discovery tool
+
-
* [[readseq]] - Reads and writes nucleic/protein sequences in various format
+
-
* [[SEALS]] - SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
+
-
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
+
-
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
+
-
* [[tRNAscan-SE]] - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
+
-
* [[WU-Blast]] - Washington U. [[BLAST]]
+
-
 
+
-
==Sequence comparisons==
+
-
 
+
-
* [[DBWatcher]] - DBWatcher is a program handling periodic [[BLAST]] searches to find similarities to your own sequences.
+
-
 
+
-
==Sequence conversion==
+
-
 
+
-
* [[readseq]] - Reads and writes nucleic/protein sequences in various format
+
-
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
+
-
 
+
-
==Sequence databases==
+
-
 
+
-
* [[ARB]] - Microbiologist's sequence database tool
+
-
 
+
-
==Sequence editor==
+
-
 
+
-
* [[gBioSeq]] - Biological sequence (ADN, protein) editor for GTK/Linux
+
-
* [[SeqPup]] - SeqPup biological sequence editor and analysis program
+
-
 
+
-
==Sequence finishing==
+
-
 
+
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
-
 
+
-
==Sequence patterns==
+
-
 
+
-
* [[Pratt]] - a pattern discovery tool
+
-
 
+
-
==Sequence similarity==
+
-
 
+
-
* [[BLAST]] - (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
+
-
 
+
-
==Sequence utilities==
+
-
 
+
-
* [[Genpak]] - a set of small utilities written in ANSI C to manipulate DNA sequences in a Unix fashion, fit for combining within shell and cgi scripts
+
-
 
+
-
==Sequencing==
+
-
 
+
-
* [[autoseq]] - a small package of base calling software for ABI automated DNA sequencers
+
-
* [[consed]] - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[phred]] - Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
+
-
 
+
-
==Smith-Waterman==
+
-
 
+
-
* [[JAligner]] - JAligner is a Java implementation of biological sequence alignment  algorithms.
+
-
* [[MPSRCH]] -  MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
+
-
 
+
-
==Solid Angle calculation==
+
-
 
+
-
* [[Steric]] - A Program to Calculate the Steric Size of Molecules about a Point in terms of their Cone Angles and Solid Angles, as well as their total Volumes and Projected Areas
+
-
 
+
-
==Statistical mechanics==
+
-
 
+
-
* [[Oslet]] - A molecular modeling and simulation environment in Java, mainly for education.
+
-
 
+
-
==Steric size calculation==
+
-
 
+
-
* [[Steric]] - A Program to Calculate the Steric Size of Molecules about a Point in terms of their Cone Angles and Solid Angles, as well as their total Volumes and Projected Areas
+
-
 
+
-
==Structural alignments==
+
-
 
+
-
* [[Deep View Swiss-PdbViewer]] - Swiss-PdbViewer is an application that provides a user          friendly interface allowing to analyse several proteins at the same time
+
-
 
+
-
==Structural biology==
+
-
 
+
-
* [[DINO]] - a realtime 3D visualization program for structural biology data.
+
-
 
+
-
==Structure==
+
-
 
+
-
* [[Abacus]] - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[caRNAsta]] - Comparative Analysis of RNA structures by Tree Alignment
+
-
* [[Chimera]] - Excellent molecular graphics package with  support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven  analysis, multiple sequence alignment analysis, multiple model analysis, dockin
+
-
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
+
-
* [[cove]] - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
* [[MODELLER]] - a program for homology protein structure modelling by satisfaction of spatial restraints.
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[MOPAC7]] - a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
+
-
* [[PyMol]] - PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
+
-
* [[RNA GENiE]] - A web based program for the prediction of rna genes in genomic DNA sequences
+
-
* [[RnaViz]] - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
+
-
 
+
-
==Structure analysis==
+
-
 
+
-
* [[Chimera]] - Excellent molecular graphics package with  support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven  analysis, multiple sequence alignment analysis, multiple model analysis, dockin
+
-
* [[CNS]] -  The 'Crystallography & NMR System' for macromolecular structure anaylsis
+
-
 
+
-
==Structure prediction==
+
-
 
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
-
==Substitution==
+
-
 
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[PHASE]] - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
+
-
 
+
-
==Substitution rates==
+
-
 
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
 
+
-
==SwissProt==
+
-
 
+
-
* [[sp2fasta]] - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
+
-
 
+
-
==Tcl/Tk==
+
-
 
+
-
* [[BioWish]] - Biowish is a C-extension for the Tcl/Tk scripting language
+
-
 
+
-
==Thermodynamics==
+
-
 
+
-
* [[caRNAc]] - RNA secondary structure inference for set of homologous sequences
+
-
* [[MELTING]] - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
+
-
 
+
-
==Threading==
+
-
 
+
-
* [[LIBELLULA]] - LIBELLULA is a neural network based web server to evaluate fold recognition results
+
-
 
+
-
==Trace==
+
-
 
+
-
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[phred]] - Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
+
-
* [[Staden Package]] - This is a free to academics (charge for commercial users) package including sequence assemble, trace viewing/editing and sequence analysis tools. It also includes a GUI to the free EMBOSS suite.
+
-
* [[UltraScan]] - UltraScan is a comprehensive GUI editing and data analysis package for hydrodynamic data from analytical ultracentrifugation experiments
+
-
 
+
-
==Trace chromatogram==
+
-
 
+
-
* [[io_lib]] - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
+
-
 
+
-
==Trace files==
+
-
 
+
-
* [[phrap]] - a program for assembling shotgun DNA sequence data
+
-
* [[phred]] - Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
+
-
 
+
-
==Trajectory analysis==
+
-
 
+
-
* [[VEGA]] -  VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D struct
+
-
 
+
-
==Transcription factors==
+
-
 
+
-
* [[GenomeInspector]] - Software for the analysis of spatial correlations of elements on DNA sequences
+
-
* [[Toucan]] - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
+
-
 
+
-
==Trees==
+
-
 
+
-
* [[ATV]] - a phylogenetic tree display tool
+
-
* [[Clann]] - Clann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree  analysis (which are used as optimality criteria) and allows exhaustive and  heuristic searches of tree-space to find the best supert
+
-
* [[fastDNAml]] - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
+
-
* [[PAML]] - Phylogenetic Analysis by Maximum Likelihood
+
-
* [[Paup]] - Software package for inference of evolutionary trees
+
-
* [[PHASE]] - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
+
-
* [[PHYLIP]] - PHYLIP is a free package of programs for inferring phylogenies.
+
-
* [[PhyloDraw]] -  PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
+
-
* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
+
-
* [[PyPhy]] - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial  genomes.
+
-
* [[unrooted]] - Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches. 
+
-
 
+
-
==Tree of life==
+
-
 
+
-
* [[PHASE]] - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
+
-
 
+
-
==Tree viewers==
+
-
 
+
-
* [[ATV]] - a phylogenetic tree display tool
+
-
* [[njplot]] - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
+
-
* [[phylowin]] - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
+
-
* [[unrooted]] - Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches. 
+
-
 
+
-
==tRNA searching==
+
-
 
+
-
* [[tRNAscan-SE]] - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
+
-
 
+
-
==Visualization==
+
-
 
+
-
* [[Friend]] - Friend, an Integrated Front-end Application for Bioinformatics
+
-
* [[Garlic]] - a free molecular visualization program
+
-
* [[GeneView II]] - Interactive GenBank Entry Visualization
+
-
* [[gff2ps]] - Converting genomic annotations in GFF format to PostScript
+
-
* [[ModView]] - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
+
-
* [[PyMol]] - PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
+
-
* [[rasmol]] - RasMol is a free program which displays molecular structure.
+
-
* [[VEGA]] -  VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D struct
+
-
* [[VMD]] - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
+
-
 
+
-
==VMD==
+
-
 
+
-
* [[NAMD]] -  NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. 
+
-
 
+
-
==Web robots==
+
-
 
+
-
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
+
-
 
+
-
==Workflow==
+
-
 
+
-
* [[Sight]] - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
+

Revision as of 23:01, 6 June 2008

Contents

0-9

A-C

D-F

G-I

J-L

M-O

P-R

S-U

V-Z

Personal tools
Namespaces
Variants
Actions
wiki navigation
Toolbox