BioEdit

BioEdit is a full integrated sequence/alignment editor. Performs translations, phylogenetic analysis, clustalw alignments, ABI trace analysis, RNA comparative analysis and BLAST searches.

URL:http://www.mbio.ncsu.edu/BioEdit/bioedit.html

BLAST

BLAST 2.0, (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.

URL:http://blast.ncbi.nlm.nih.gov/Blast.cgi

BOXSHADE

BOXSHADE is a program for creating good looking printouts from multiple-aligned protein or DNA sequences. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor.

URL:ftp://www.isrec.isb-sib.ch/pub/

Circle

Infer RNA secondary structure using the comparative method.
URL:http://taxonomy.zoology.gla.ac.uk/rod/circles/

ClustalW

Clustal-W is a multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.

URL:ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

ClustalX

ClustalX is a new windows interface for the ClustalW. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.

URL:ftp://ftp.ebi.ac.uk/pub/software/dos/clustalx/

Dambe

It is a general-purpose package for DNA and protein sequence phylogenies, and also gene frequencies.
URL:http://aix1.uottawa.ca/~xxia/software/software.htm

DCSE

DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment.

URL:http://rrna.uia.ac.be/dcse/

DNA Tools

DNATools is a comprehensive program package for routine handling and analysis of nucleotide and protein sequences. The program includes functions for batch renaming, editing and annotating sequences, restriction mapping, translation, automated blast search and information retrieval, codon analysis, primer design and ordering and a lot more...

URL:http://www.crc.dk/dnatools/

DNA Club

PC program for Integrated analysis on DNA sequences.

URL: http://softwareseek.progenote.net/downloads/

EMBOSS

EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis.

URL: http://emboss.sourceforge.net/

FastA

The FastA program has been developed by Pearson & Lipman (1988) and is useful to find all protein sequences of a database such as Swiss-Prot, that are homologous to a given sequence.

URL: http://www.ebi.ac.uk/fasta33/

FreeTree

Freeware program for construction and bootstrap (and jackknife) analysis of phylogenetic trees from binary data (RAPD, RFLP, AFLP etc.)

URL: http://www.natur.cuni.cz/~flegr/programs/freetree.htm

GeneDoc

GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.

URL: http://www.psc.edu/biomed/genedoc/

GeneTree

GeneTree is an experimental program for comparing gene and species trees.

URL:http://www.stats.ox.ac.uk/~griff/software.html

HMMER

A profile hidden Markov model that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.

URL:http://hmmer.wustl.edu/

HyPhy

It intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more...

URL: http://www.hyphy.org/

JalView

Graphical multiple alignment editor. Requires Java Virtual Machine.

URL: http://www.jalview.org/

JEMBOSS

Jemboss is developed by the EMBOSS team. The software is free and part of the EMBOSS distribution.

URL:http://emboss.sourceforge.net/Jemboss/

Mega3

MEGA is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

URL:http://www.megasoftware.net/

MFold

Mfold is an RNA and DNA folding package.

URL:http://www.bioinfo.rpi.edu/~zukerm/export/mfold-3.html

NCBI ToolKit

The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.

URL: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/

PHYLIP

PHYLIP is a free package of programs for inferring phylogenies.

URL: http://evolution.genetics.washington.edu/phylip.html

PhyloDraw

PhyloDraw is a drawing tool for creating phylogenetic trees. It supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams.

URL: http://pearl.cs.pusan.ac.kr/phylodraw/

RNA DRAW

It is an integrated program for RNA secondary structure calculation and analysis.

URL: http://www.rnadraw.com/

Readseq

Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.

URL: http://iubio.bio.indiana.edu/soft/molbio/readseq/

Seaview

SeaView is a graphical multiple sequence alignment editor. It is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.

URL: http://pbil.univ-lyon1.fr/software/seaview.html

Sequence Manipulation Suite

The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.

URL: http://bioinformatics.org/sms2/

TreeView

TreeView X is an open source program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs).

URL: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/index.html

Vienna RNA Package

RNA Secondary Structure Prediction and Comparison.

URL: http://www.tbi.univie.ac.at/~ivo/RNA/

WinGene

A tool for the analysis of nucleotide sequences.

URL: http://www.ipw.agrl.ethz.ch/~lhennig/wingene.html

X3DNA

3DNA is a versatile package for analyzing and rebuilding three-dimensional nucleic acid structures, based on a standard reference frame.

URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/

Artemis

Artemis is a free genome 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.

URL: http://www.sanger.ac.uk/Software/Artemis/

Chromas

It will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create.

URL: http://www.technelysium.com.au/chromas.html

GenAl

GenAl is a program for genomic alignment, i.e. alignment of DNA sequences with coding regions. It is an implementation of the heuristic algorithm described in Hein, J. & J. Stoevlbaek (1994): Genomic Alignment. J. Mol. Evol.

URL: ftp://ftp.ebi.ac.uk/pub/software/unix/

Glimmer

A system for finding genes in microbial DNA, especially the genomes of bacteria and archaea.Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.

URL:http://www.tigr.org/software/glimmer/

Glimmer HMM

A fast and accurate gene finder based on a GHMM architecture,
developed specifically for eukaryotes. It incorporates splice site models adapted from the GeneSplicer program and uses interpolated Markov models for evaluating the coding regions.

URL: http://www.tigr.org/software/GlimmerHMM/

Glimmer M

A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programming algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The decision about what gene model is best is a combination of the strength of the splice sites and the score of the exons generated by an interpolated Markov model (IMM).

URL: http://www.tigr.org/software/glimmerm/

MUMmer

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

URL: http://www.tigr.org/software/mummer/

pDRAW

pDRAW32 is being developed as a free time hobby project. It is far from finished, but as it has reached a point where it could be helpful for many labs, it is now available to the scientific community.

URL:http://www.acaclone.com/

PrimerDesign

Primer Design is a DOS-program to choose primer for PCR or oligonucleotide probes. It is tailored to check known sequences for repeats and unique sequences and subsequently to create prober primers according to this data. A lot of constrains are available to meet your conditions. It can handle up to 32000 base pairs.

URL: http://www.bioinf-club.com/software/

Sequin

Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, segmented sets of DNA, or phylogenetic and population studies.

URL: http://www.ncbi.nlm.nih.gov/Sequin/

Staden

The Staden Package consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin).

URL: http://staden.sourceforge.net/

ADVICE

Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of the proteins. It is suggested that co-evolution of proteins is useful for predicting and validating protein-protein interactions.

URL: http://advice.i2r.a-star.edu.sg/

ANTHEPROT

ANTHEPROT (ANalyse THE PROTeins) is to integrate into a single package most of the methods designed for protein sequence analysis.

URL: http://antheprot-pbil.ibcp.fr/

CNplot

CNplot is a network visualization tool that can be used for large-scale networks, as long as they are pre-clustered.

URL: http://csb.stanford.edu/~nbatada/VCN.html

Graphviz

Graph layout software for protein network.

URL: http://www.graphviz.org/

InterViewer

InterWeaver is a tool employing two approaches to detect potential protein interactions by searching for and interpreting evidence available from on-line databases. The first approach finds homologues for a sequence and searches for interacting partners in protein interaction and literature databases, and the second finds sequence domains, and then searches for domain fusion events and possible domain interactions.

URL: http://wilab.inha.ac.kr/protein/

Osprey

Application for graphically representing physical and genetic biological interactions; is coupled with the General Repository of Interaction Datasets (The GRID); available for Unix and Windows.

URL: http://biodata.mshri.on.ca/osprey/servlet/Index

Pajek

Program for Larger Network Analysis.

URL: http://vlado.fmf.uni-lj.si/pub/networks/pajek/default.htm

PIN

To visualize the protein's interaction and function annotations. The software allows the user to search for information on putative protein interactions and function classes.

URL: http://www.bioinfo.org.cn/PIN/

Teverna

Taverna is a tool for creating and running bioinformatics workflows.

URL: http://taverna.sourceforge.net/

WinPep

A versatile tool for the analysis of amino acid sequences.

URL: http://www.ipw.agrl.ethz.ch/~lhennig/winpep.html

Cellware

Cellware has been designed to conduct modeling and simulation of gene regulatory and metabolic pathways and also offer an integrated environment for diverse mathematical representations, parameter estimation and optimization. In addition, a user-friendly graphical display and capability to run large and complex models would be provided by default. A very special feature of Cellware is that it would be the first grid based modeling and simulation tool in the field of Systems Biology.

URL: http://www.bii.a-star.edu.sg/research/sbg/cellware/

CytoScape

Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.

URL: http://www.cytoscape.org/

E-Cell 3

E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.

URL: http://www.e-cell.org/

Gepasi

Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis.

URL: http://www.gepasi.org/

3D-Dock Suite

[FTDock, RPScore and MultiDock]

FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information.

URL: http://www.bmm.icnet.uk/docking/

ArgusLab

It is an incredible molecular modeling, graphics, and drug design program.

URL: http://www.planaria-software.com/

Biodesigner

It is a molecular modeling and visualization program for personal computers which is capable of creating homologous models of proteins, evaluate, and refine the models.

URL: http://www.pirx.com/biodesigner/index.shtml

Chem2Pac

Chem2Pac is intended to be a kind of computational chemistry integrator, which has a multiple document interface, a molecular rendering utility, and allows the manipulation of various files.

URL: http://www.ifi.unicamp.br/gsonm/chem2pac/

Cn3D

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.

URL: http://ncbi.nih.gov/Structure/CN3D/cn3d.shtml

Dang

Dang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base. In its most basic form, it writes out dihedral angles (phi, psi, chi) hence the name. The output is formatted for easy parsing by awk, grep, sort and other UNIX utilities.

URL: http://kinemage.biochem.duke.edu/software/dang.php

DomainFinder

It is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes ease of use: a state-of-the-art graphical user interface export of results for visualization and further analysis (VRML, PDB, and MMTK object format).

URL: http://dirac.cnrs-orleans.fr/DomainFinder/

Easy Winbabel

It's a program for chemists and physicists dealing with molecular modeling. It uses the well known BABEL program as basis and provides a windows interface. The zip file includes BABEL ver 1.6.

URL: http://users.uoi.gr/nkourkou/babel.html

EDPDB

EdPDB is a program to manipulate and extract information from Brookhaven Protein Databank (PDB) format coordinate file(s) of three-dimensional protein structures.

URL: http://omega.omrf.ouhsc.edu/zhangc/edpdb/edpdb.html

Garlic

It is a free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software.

URL: http://garlic.mefos.hr/garlic-1.0/

Ghemical

Ghemical is a computational chemistry software package released under the GNU GPL. Geometry optimization, molecular dynamics and some visualization tools are currently available. If quantum-mechanical calculations are needed, Ghemical can be directly linked into the quantum chemistry program MPQC (which is also distributed under GNU GPL). Therefore Ghemical can serve as a graphical front-end for the MPQC program, currently providing various 3D-plots for electron densities, molecular orbitals and molecular orbital densities.

URL: http://www.uku.fi/~thassine/ghemical/

gOpenMol

gOpenMol graphics interface to the OpenMol and can be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbital's, electron densities and electrostatic potentials.

URL: http://www.csc.fi/gopenmol/

GRAMM

GRAMM is a program for protein docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules. The molecular pairs may be: two proteins, a protein and a smaller compound, two transmembrane helices, etc. GRAMM may be used for high-resolution molecules, for inaccurate structures (where only the gross structural features are known), in cases of large conformational changes, etc.

URL: http://www.chem.ac.ru/Chemistry/Soft/GRAMM.en.html

GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

URL: http://www.gromacs.org/

HEX

Hex is an interactive protein docking and molecular superposition program. Currently, Hex understands protein and DNA structures in PDB format.  <!--[if !supportLineBreakNewLine]-->
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URL: http://www.csd.abdn.ac.uk/hex/

KineMage

A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated.

URL: http://kinemage.biochem.duke.edu/kinemage/magepage.php

LOOPP

LOOPP is a fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure.

URL: http://cbsu.tc.cornell.edu/software/loopp/index.htm

MOIL

MOIL is a molecular modeling software, which is in the public domain, and is written in the group of Ron Elber. Available features, such as energy calculations, minimization and calculations of classical trajectories. Graphic User Interface for a wide range of moil applications on a Windows desktop. This interface enables direct calculation on a desktop, on a Windows cluster, and on properly configured web servers.

URL: http://cbsu.tc.cornell.edu/software/moil/moil.html

MOLMOL

MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.

URL: http://hugin.ethz.ch/wuthrich/software/molmol/

Molscript

A program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.

URL: http://www.avatar.se/molscript/

NAMD

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code.

URL: http://www.ks.uiuc.edu/Research/namd/

NOC

TOP

It is a free program for protein structure model-building, visualization, validation and analysis.

URL: http://noc.ibp.ac.cn/

OpenBable

Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.

URL: http://openbabel.sourceforge.net/

Rasmol

Rasmol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules.

URL: http://www.umass.edu/microbio/rasmol/index2.htm

Raster 3D

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware.

URL: http://www.bmsc.washington.edu/raster3d/raster3d.html

Reduce

Reduce is a program for adding hydrogens to a Protein Data Bank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided. A slightly modified version of the connectivity table published by the PDB is included (reduce_het_dict.txt).

URL: http://kinemage.biochem.duke.edu/software/reduce.php

SPDBViewer

Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

URL: http://au.expasy.org/spdbv/

TraX

TraX (Trajectory eXplorer) is a simple Biodesigner-like program working under Linux and Windows. The program allows reading a protein folding simulation trajectory (TRA file) and saving a single frame as a PDB file.

URL: http://www.pirx.com/biodesigner/download.html

VEGA

VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modeling suite.

URL: http://users.unimi.it/~ddl/

BioKnoppix

Bioknoppix is a customized distribution of Knoppix Linux Live CD. With this distribution you just boot from the CD and you have a fully functional Linux OS distribution with open source applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesn't touch the host computer, being ideal for demonstrations, molecular biology students, workshops, etc.

URL: http://bioknoppix.hpcf.upr.edu/

BLAST-Server

A BLAST server ready to run. Just pop the CD, boot the computer and you have a BLAST server . BLAST is one of the most useful bioinformatics application.

URL: http://www.genesdigitales.com/blastoncd/

DNA Linux

DNALinux is a Linux distribution with bioinformatics software pre-installed. DNA and protein sequence manipulation software is included. Like EMBOSS, Primer3, ClustalW, T-Coffe and others.

URL: http://www.dnalinux.com/

Vigyaan

Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software.

URL: http://www.vigyaancd.org/

V-Linux

VLinux Bioinformatics workbench is a Linux distribution for Bioinformatics. It is easy to use, no installation required, CD-based distribution based on Knoppix 3.3. It includes a variety of sequence and structure analysis packages.

URL: http://bioinformatics.org/vlinux/index.ph

BioJava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

URL: http://www.biojava.org/

BioMOBY

An international group of biological data hosts, biological data service providers, and coders whose aim is to set standards for biological data representation, distribution, and discovery.

URL: http://biomoby.org/

BioPerl

Bioperl is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.

URL: http://bio.perl.org/

BioPipe

The biopipe is a workflow framework that seeks to address some of the complexity involved in carrying out large scale bioinformatics analysis. It has been designed to work intimately with the bioperl package. The main idea behind biopipe is to enable users to integrate data from disparate sources into a common analysis framework. In addition, it is designed to work over a compute farm providing job management functionality. This project was extended borrowing code and concepts from the Ensembl pipeline project.

URL: http://biopipe.org/

BioPython

An international association of developers of freely available Python tools for computational molecular biology. biopython.org provides an online resource for modules, scripts, and web links for developers of Python based software for life science research.

URL: http://www.biopython.org/

BioRuby

BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. The BioRuby library follows the KISS principle in order to maximize its usability and efficiency for biologists as a daily tool.

URL: http://bioruby.org