From Bioinformatics.Org Wiki
Revision as of 23:07, 16 May 2007 by Jeff
- Abacus - ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure.
- Acedb - Acedb is a genome database system originally developed for the C.elegans genome project
- AMMP - a modern full-featured molecular mechanics, dynamics and modeling program.
- Amplicon - Program for designing group-specific PCR primer sets
- Angler - A Browser of C.elegans Embryo Development In Time and Space
- ARB - Microbiologist's sequence database tool
- Arka - graphical interface for the programs from the GP (Genpak) package
- 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.
- ATV - a phylogenetic tree display tool
- autoseq - a small package of base calling software for ABI automated DNA sequencers
- Babel - a program designed to interconvert a number of file formats currently used in molecular modeling
- 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.
- Biolisp - BioLisp.org is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences.
- BioMail - automate searching for recent scientific papers in the PubMed Medline database
- Bioperl - open source Perl tools for bioinformatics, genomics and life science research
- 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 - BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
- 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.
- 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
- 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, including flexible molecular graphics, high resolution images for publication, user-driven analysis, multiple sequence alignment analysis, multiple model analysis, dockin
- Clann - Clann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree analysis (which are used as optimality criteria) and allows exhaustive and heuristic searches of tree-space to find the best supertree
- Clustal W - The famous multiple alignment program
- Clustal X - Provides a window-based user interface to the Clustal W multiple alignment program
- CNS - The 'Crystallography & NMR System' for macromolecular structure anaylsis
- consed - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
- ConsInspector - A tool for the prediction of protein binding sites in nucleic acids
- cove - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
- DBWatcher - DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences.
- 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
- DINO - a realtime 3D visualization program for structural biology data.
- DNA-GUI - DNA Graphical User Interface
- DomainFinder - DomainFinder 1.0 DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins
- EMBOSS - EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
- Ensembl - software system which produces and maintains automatic annotation on eukaryoticgenomes
- fastDNAml - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
- Friend - Friend, an Integrated Front-end Application for Bioinformatics
- Garlic - a free molecular visualization program
- gBioSeq - Biological sequence (ADN, protein) editor for GTK/Linux
- GDE - The GDE is a set of programs for multiple sequence alignment and analysis.
- GDIS - a GTK based program for the display and manipulation of isolated molecules and periodic systems
- GEANFAMMER - GEnome ANalysis and Protein FAMily MakER
- 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.
- GeneView II - Interactive GenBank Entry Visualization
- GenomeInspector - Software for the analysis of spatial correlations of elements on DNA sequences
- GenomePixelizer - Genome Visualization Tool: Detection of duplicating events in genomes, Displaying the Genetic Maps, Comparative genetics in general.
- 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
- gff2ps - Converting genomic annotations in GFF format to PostScript
- GRIL - GRIL automates the process of identifying large-scale genome inversions and rearrangements
- Gromacs - The World' s fastest Molecular Dynamics - and it' s GPL
- GRS - A Graphic Tool for Genome Retrieval and Segment Analysis
- HMMER - Profile hidden Markov models for biological sequence analysis
- io_lib - An open source C library of sequence trace files supporting ABI, ALF, SCF, CTF and ZTR file formats.
- JAligner - JAligner is a Java implementation of biological sequence alignment algorithms.
- Jalview - Jalview - a java multiple alignment editor
- Kintecus - Run chemical kinetics/fitting of catalyst reactor, and enzyme reactions
- Leksbot - an explanatory dictionary of botanic and biological terms
- LIBELLULA - LIBELLULA is a neural network based web server to evaluate fold recognition results
- 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.
- 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.
- Mauve - Mauve is a multiple genome alignment and visualization package that considers large-scale rearrangements in addition to nucleotide substitution and indels.
- MELTING - Accurate computation of the enthalpy, entropie and melting temperature of a nucleic acid duplex
- MeltSim - Calculation of DNA melting curves and maps using the Poland-Scheraga algorithm and empirical constraints by R.D. Blake.
- MMTK-2.2 - molecular modeling tool-kit 2.2
- 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.
- MOLPHY - A Computer Program Package for Molecular Phylogenetics including ProtML
- MOPAC7 - a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
- mpiBLAST - mpiBLAST is a parallel implementation of NCBI-BLAST that uses database segmentation. It achieves a super-linear speedup in some cases.
- MPSRCH - MPSRCH (tm) is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
- MSPcrunch - a BLAST enhancement filter
- Musca - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
- MUSCLE - Multiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
- NAMD - NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
- NCRNASCAN - a structural RNA genefinder
- njplot - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
- OmniGene - Standardizing Biological Data Interchange Through Web Services Technology
- On-line Genome Annotations - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features
- Oslet - A molecular modeling and simulation environment in Java, mainly for education.
- PAML - Phylogenetic Analysis by Maximum Likelihood
- 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
- 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.
- 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.
- 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.
- PKNOTS - RNA pseudoknot prediction
- Populations - Population genetic software (individuals or populations distances, phylogenetic trees)
- Pratt - a pattern discovery tool
- primer - a program for picking primers for PCR reaction
- ProSA - ProSA is a useful web application for finding known protein domains in nucleotide/protein sequences via PROSITE database searching
- 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.
- PyPhy - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
- rasmol - RasMol is a free program which displays molecular structure.
- readseq - Reads and writes nucleic/protein sequences in various format
- 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
- 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
- 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
- SeqPup - SeqPup biological sequence editor and analysis program
- ShadyBox - The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
- Sight - Allows programming free assembling of web resoureces, local executables and ssh services into arbitrary workflow.
- sp2fasta - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
- Spock - a full-featured molecular graphics program
- 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.
- 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
- Teiresias-based Association Discovery - Discover associations in your data set (gene expression analysis, phenotype analysis, etc.)
- Teiresias-based Gene expression analysis - Discover patterns in microarray data using the Teiresias algorithm. Allows discovery of inversely regulated genes.
- Toucan - A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
- TREE-PUZZLE - Maximum likelihood analysis for nucleotide, amino acid, and two-state data
- 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
- 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.
- 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
- VEIL - A hidden Markov model for finding genes in vertebrate DNA\ufffd
- Vienna RNA Package - RNA Secondary Structure Prediction and Comparison
- VMD - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
- WHAT IF - WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc
- WU-Blast - Washington U. BLAST
- XMolCalc - a small utility that allows you to calculate a molecular weight
- xsact - EST clustering tool
- ZDOCK - Protein-protein complex structure prediction software