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Sequence Analysis:

BioEdit TOP

BioEdit is a full integrated sequence/alignment editor.

Performs translations, phylogenetic analysis, clustalwalignments, ABI trace analysis, RNA comparativeanalysis and BLAST searches.

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

BLAST TOP

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

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

BOXSHADE TOP

BOXSHADE is a program for creating good looking

printouts from multiple-aligned protein or DNAsequences. The program does no alignment by itself,it has to take as input a file preprocessed by amultiple alignment program or a multiple file editor.

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

Circle TOP

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

ClustalW TOP

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

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

ClustalX TOP

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

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

Dambe TOP

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

DCSE TOP

DCSE (Dedicated Comparative Sequence Editor) is amultiple alignment editor. It can be used to editprotein, DNA or RNA alignments. The structure of themolecules can be incorporated in the alignment.

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

DNA Tools TOP
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DNATools is a comprehensive program package forroutine handling and analysis of nucleotide andprotein sequences. The program includes functions for

batch renaming, editing and annotating sequences,restriction mapping, translation, automated blastsearch and information retrieval, codon analysis,primer design and ordering and a lot more...

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

DNA Club TOP

PC program for Integrated analysis on DNAsequences.

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

EMBOSS TOP

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 TOP

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

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

FreeTree TOP

Freeware program for construction and bootstrap(and jackknife) analysis of phylogenetic trees frombinary data (RAPD, RFLP, AFLP etc.)
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URL:http://www.natur.cuni.cz/~flegr/programs/freetree.htm

GeneDoc TOP

GeneDoc does sequence alignment editing andshading, as well as secondary structure shading andsuper family group support.

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

GeneTree TOP

GeneTree is an experimental program for comparing

gene and species trees.

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

HMMER TOP

A profile hidden Markov model that can be used to dosensitive database searching using statisticaldescriptions of a sequence family's consensus.

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

HyPhy TOP

It intended to perform maximum likelihood analysesof genetic sequence data and equipped with tools totest various statistical hypotheses. HYPHY wasdesigned with maximum flexibility in mind and to that

end it incorporates a simple high level programminglanguage which enables the user to tailor theanalyses precisely to his or her needs. These includerelative rate and ratio tests, several methods of ML

based phylogeny reconstruction, bootstrapping,model selection, positive selection, molecular clocktests and many more...

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

Graphical multiple alignment editor. Requires JavaVirtual Machine.

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

JEMBOSS TOP

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

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

Mega3 TOP

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 evolutionaryhypotheses.

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

MFold TOP

Mfold is an RNA and DNA folding package.

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

NCBI ToolKit TOP

The NCBI Software Development Toolkit was

developed for the production and distribution of
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GenBank, Entrez, BLAST, and related services by

NCBI.

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

PHYLIP TOP

PHYLIP is a free package of programs for inferring

phylogenies.

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

PhyloDraw TOP

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 TOP

It is an integrated program for RNA secondarystructure calculation and analysis.

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

Readseq TOP

Reads and writes nucleic/protein sequences invarious formats. Data files may have multiplesequences.

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

SeaView is a graphical multiple sequence alignmenteditor. It is able to read and write various alignmentformats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP,

MASE). It allows to manually edit the alignment, andalso to run DOT-PLOT or CLUSTALW programs tolocally improve the alignment.

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

SequenceManipulation

SuiteTOP

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 TOP

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 RNAPackage TOP

RNA Secondary Structure Prediction and Comparison.

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

A tool for the analysis of nucleotide sequences.

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

X3DNA TOP

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

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

Genomics:

Artemis TOP

Artemis is a free genome viewer and annotation toolthat allows visualization of sequence features and theresults of analyses within the context of thesequence, and its six-frame translation.

URL:

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

Chromas TOP

It will display and prints chromatogram files from ABIautomated DNA sequencers, and Staden SCF fileswhich the analysis programs for ALF, Li-Cor andVisible Genetics OpenGene sequencers can create.

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

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

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

Glimmer TOP

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 TOP

A fast and accurate gene finder based on a GHMMarchitecture,developed specifically for eukaryotes. It incorporatessplice site models adapted from the GeneSplicerprogram and uses interpolated Markov models forevaluating the coding regions.

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

Glimmer M TOP

A gene finder derived from Glimmer, but developedspecifically for eukaryotes. It is based on a dynamicprogramming algorithm that considers all
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combinations of possible exons for inclusion in a genemodel 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 thescore of the exons generated by an interpolatedMarkov model (IMM).

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

MUMmer TOP

MUMmer is a system for rapidly aligning entire

genomes, whether in complete or draft form.

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

pDRAW TOP

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

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

PrimerDesignTOP

Primer Design is a DOS-program to choose primer forPCR or oligonucleotide probes. It is tailored to checkknown sequences for repeats and unique sequencesand subsequently to create prober primers accordingto this data. A lot of constrains are available to meetyour conditions. It can handle up to 32000 base pairs.

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

Sequin TOP

Sequin is a stand-alone software tool developed bythe NCBI for submitting and updating entries to the
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GenBank, EMBL, or DDBJ sequence databases. It iscapable of handling simple submissions that contain asingle short mRNA sequence, and complex

submissions containing long sequences, multipleannotations, segmented sets of DNA, or phylogeneticand population studies.

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

Staden TOP

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

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

ADVICE TOP

Automated Detection and Validation of Interaction byCo-Evolution (ADVICE) takes a list of proteinsequences or sequence pairs as input and usesorthologous sequences to assess the similarity in theevolutionary history of the proteins. It is suggestedthat co-evolution of proteins is useful for predictingand validating protein-protein interactions.

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

ANTHEPROT TOP

ANTHEPROT (ANalyse THE PROTeins) is to integrateinto a single package most of the methods designedfor protein sequence analysis.

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

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

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

Graphviz TOP

Graph layout software for protein network.

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

InterViewer TOP

InterWeaver is a tool employing two approaches todetect potential protein interactions by searching forand interpreting evidence available from on-linedatabases. The first approach finds homologues for asequence and searches for interacting partners inprotein interaction and literature databases, and thesecond finds sequence domains, and then searchesfor domain fusion events and possible domain

interactions.

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

Osprey TOP

Application for graphically representing physical andgenetic biological interactions; is coupled with theGeneral Repository of Interaction Datasets (TheGRID); available for Unix and Windows.

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

Pajek TOP

Program for Larger Network Analysis.
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URL: http://vlado.fmf.uni-lj.si/pub/networks/pajek/default.htm

PIN TOP

To visualize the protein's interaction and functionannotations. The software allows the user to searchfor information on putative protein interactions andfunction classes.

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

Teverna TOP

Taverna is a tool for creating and runningbioinformatics workflows.

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

WinPep TOP

A versatile tool for the analysis of amino acid

sequences.

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

Systems Biology:

Cellware TOP

Cellware has been designed to conduct modeling andsimulation of gene regulatory and metabolic pathwaysand also offer an integrated environment for diversemathematical representations, parameter estimationand optimization. In addition, a user-friendlygraphical display and capability to run large andcomplex models would be provided by default. A veryspecial feature of Cellware is that it would be the firstgrid based modeling and simulation tool in the field of
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Systems Biology.

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

CytoScape TOP

Cytoscape is a visualization platform for use withmolecular interaction networks. Interaction data canbe integrated with other state data such as geneexpression profiles. The input to Cytoscape includeslists of interaction pairs, and tab/space delimited files

containing mRNA expression profiles. The nodes ofthe interaction networks can be filtered by suchvariables as GO annotations and number ofinteractions.

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

E-Cell 3 TOP

E-Cell Project is an international research projectaiming to model and reconstruct biologicalphenomena in silico, and developing necessarytheoretical supports, technologies and softwareplatforms to allow precise whole cell simulation.

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

Gepasi TOP

Gepasi is a software package for modelingbiochemical systems. It simulates the kinetics ofsystems of biochemical reactions and provides anumber of tools to fit models to data, optimize anyfunction of the model, perform metabolic control

analysis and linear stability analysis.

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

Molecular Modeling:
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3D-Dock

Suite TOP

[FTDock, RPScore and MultiDock]

FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predicttheir correct binding geometry. FTDock outputsmultiple predictions that can be screened usingbiochemical information.

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

ArgusLab TOP

It is an incredible molecular modeling, graphics, anddrug design program.

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

Biodesigner TOP

It is a molecular modeling and visualization programfor personal computers which is capable of creatinghomologous models of proteins, evaluate, and refinethe models.

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

Chem2Pac TOP

Chem2Pac is intended to be a kind of computationalchemistry integrator, which has a multiple documentinterface, a molecular rendering utility, and allows

the manipulation of various files.

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

Cn3D TOP
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Cn3D is a helper application for your web browserthat allows you to view 3-dimensional structures fromNCBI's Entrez retrieval service.

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

Dang TOP

Dang reads coordinates from a Protein DataBank(PDB) molecular structure file and generates a tableof several useful geometric measurements for each

residue or base. In its most basic form, it writes outdihedral angles (phi, psi, chi) hence the name. Theoutput is formatted for easy parsing by awk, grep,sort and other UNIX utilities.

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

DomainFinderTOP

It is an interactive program for the determination andcharacterization of dynamical domains in proteins. Itskey features are computational efficiency: even largeproteins can be analyzed using a desktop computer ina few minutes ease of use: a state-of-the-art

graphical user interface export of results forvisualization and further analysis (VRML, PDB, andMMTK object format).

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

Easy

Winbabel TOP

It's a program for chemists and physicists dealing

with molecular modeling. It uses the well knownBABEL program as basis and provides a windowsinterface. The zip file includes BABEL ver 1.6.

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

EdPDB is a program to manipulate and extractinformation 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 TOP

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

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

Ghemical TOP

Ghemical is a computational chemistry softwarepackage released under the GNU GPL. Geometryoptimization, molecular dynamics and somevisualization tools are currently available. Ifquantum-mechanical calculations are needed,Ghemical can be directly linked into the quantumchemistry program MPQC (which is also distributedunder GNU GPL). Therefore Ghemical can serve as agraphical front-end for the MPQC program, currentlyproviding various 3D-plots for electron densities,molecular orbitals and molecular orbital densities.

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

gOpenMol TOP

gOpenMol graphics interface to the OpenMol and canbe used for the analysis and display of moleculardynamics trajectories and the display of molecularorbital's, electron densities and electrostaticpotentials.

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

GRAMM is a program for protein docking. To predictthe structure ofa complex, it requires only the atomiccoordinates of the two molecules (no informationabout the binding sites is needed). The programperforms an exhaustive 6-dimensional search throughthe relative translations and rotations of themolecules. The molecular pairs may be: two proteins,a protein and a smaller compound, twotransmembrane helices, etc. GRAMM may be used forhigh-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 TOP

GROMACS is a versatile package to perform moleculardynamics, i.e. simulate the Newtonian equations ofmotion for systems with hundreds to millions ofparticles.

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

HEX TOP

Hex is an interactive protein docking and molecularsuperposition program. Currently, Hex understandsprotein and DNA structures in PDB format.

URL: http://www.csd.abdn.ac.uk/hex/

KineMage TOP

A "kinemage" (kinetic image) is a scientificillustration presented as an interactive computer
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display. Operations on the displayed kinemagerespond immediately: the entire image can be rotatedin real time, parts of the display can be turned on or

off, points can be identified by selecting them, andthe change between different forms can be animated.

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

LOOPP TOP

LOOPP is a fold recognition program based on thecollection of numerous signals, merging them into asingle score, and generating atomic coordinatesbased on an alignment into a homologue templatestructure.

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

MOIL TOP

MOIL is a molecular modeling software, which is inthe public domain, and is written in the group of RonElber. Available features, such as energy calculations,minimization and calculations of classical trajectories.Graphic User Interface for a wide range of moilapplications on a Windows desktop. This interfaceenables direct calculation on a desktop, on a Windowscluster, and on properly configured web servers.

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

MOLMOL TOP

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/
http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://kinemage.biochem.duke.edu/kinemage/magepage.phphttp://kinemage.biochem.duke.edu/kinemage/magepage.phphttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://cbsu.tc.cornell.edu/software/loopp/index.htmhttp://cbsu.tc.cornell.edu/software/loopp/index.htmhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://cbsu.tc.cornell.edu/software/moil/moil.htmlhttp://cbsu.tc.cornell.edu/software/moil/moil.htmlhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://kinemage.biochem.duke.edu/kinemage/magepage.phphttp://kinemage.biochem.duke.edu/kinemage/magepage.phphttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://cbsu.tc.cornell.edu/software/loopp/index.htmhttp://cbsu.tc.cornell.edu/software/loopp/index.htmhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://cbsu.tc.cornell.edu/software/moil/moil.htmlhttp://cbsu.tc.cornell.edu/software/moil/moil.htmlhttp://www.rishibiotech.com/biotools.htm#biotools%23biotools


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Molscript TOP

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

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

NAMD TOP

NAMD, recipient of a 2002 Gordon Bell Award, is aparallel molecular dynamics code designed for high-performance simulation of large biomolecularsystems. Based on Charm++ parallel objects, NAMDscales to hundreds of processors on high-end parallelplatforms and tens of processors on commodityclusters using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and isdistributed 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 TOP

Open Babel is a project designed to pick up whereBabel left off, as a cross-platform program and librarydesigned to interconvert between many file formats

used in molecular modeling and computationalchemistry.

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

Rasmol TOP
http://hugin.ethz.ch/wuthrich/software/molmol/http://hugin.ethz.ch/wuthrich/software/molmol/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.avatar.se/molscript/http://www.avatar.se/molscript/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.ks.uiuc.edu/Research/namd/http://www.ks.uiuc.edu/Research/namd/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://noc.ibp.ac.cn/http://noc.ibp.ac.cn/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://openbabel.sourceforge.net/http://openbabel.sourceforge.net/http://hugin.ethz.ch/wuthrich/software/molmol/http://hugin.ethz.ch/wuthrich/software/molmol/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.avatar.se/molscript/http://www.avatar.se/molscript/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.ks.uiuc.edu/Research/namd/http://www.ks.uiuc.edu/Research/namd/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://noc.ibp.ac.cn/http://noc.ibp.ac.cn/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://openbabel.sourceforge.net/


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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 TOP

Raster3D is a set of tools for generating high qualityraster images of proteins or other molecules. The coreprogram renders spheres, triangles, cylinders, andquadric surfaces with specular highlighting, Phongshading, and shadowing. It uses an efficient softwareZ-buffer algorithm which is independent of anygraphics hardware.

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

Reduce TOP

Reduce is a program for adding hydrogens to a

Protein Data Bank (PDB) molecular structure file.Hydrogens are added in standardized geometry withoptimization ofthe orientations of OH, SH, NH3+, Met

methyls, Asn and Gln sidechain amides, and His rings.Both proteins and nucleic acids can be processed. HETgroups can also be processed as long as the atomconnectivity is provided. A slightly modified version ofthe connectivity table published by the PDB isincluded (reduce_het_dict.txt).

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

SPDBViewer TOP

Swiss-PdbViewer is an application that provides auser friendly interface allowing to analyze severalproteins at the same time. The proteins can besuperimposed in order to deduce structuralalignments and compare their active sites or anyother relevant parts. Amino acid mutations, H-bonds,angles and distances between atoms are easy toobtain thanks to the intuitive graphic and menu
http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.umass.edu/microbio/rasmol/index2.htmhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.bmsc.washington.edu/raster3d/raster3d.htmlhttp://www.bmsc.washington.edu/raster3d/raster3d.htmlhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://kinemage.biochem.duke.edu/software/reduce.phphttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.umass.edu/microbio/rasmol/index2.htmhttp://www.umass.edu/microbio/rasmol/index2.htmhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.bmsc.washington.edu/raster3d/raster3d.htmlhttp://www.bmsc.washington.edu/raster3d/raster3d.htmlhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://kinemage.biochem.duke.edu/software/reduce.phphttp://kinemage.biochem.duke.edu/software/reduce.phphttp://www.rishibiotech.com/biotools.htm#biotools%23biotools


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interface.

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

TraX TOP

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

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

VEGA TOP

VEGA was originally developed to create a bridgebetween most of the molecular software packagesonly, but in the years, enhancing its features, it's

evolved to a complete molecular modeling suite.

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

:

BioKnoppix TOP

Bioknoppix is a customized distribution of KnoppixLinux Live CD. With this distribution you just bootfrom the CD and you have a fully functional Linux OSdistribution with open source applications targeted

for the molecular biologist. Beside using some RAM,Bioknoppix doesn't touch the host computer, beingideal for demonstrations, molecular biology students,

workshops, etc.

URL: http://bioknoppix.hpcf.upr.edu/
http://au.expasy.org/spdbv/http://au.expasy.org/spdbv/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.pirx.com/biodesigner/download.htmlhttp://www.pirx.com/biodesigner/download.htmlhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://au.expasy.org/spdbv/http://au.expasy.org/spdbv/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.pirx.com/biodesigner/download.htmlhttp://www.pirx.com/biodesigner/download.htmlhttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://users.unimi.it/~ddl/http://www.rishibiotech.com/biotools.htm#biotools%23biotools


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BLAST-

Server TOP

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

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

DNA Linux TOP

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

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

Vigyaan TOP

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

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

V-Linux TOP

VLinux Bioinformatics workbench is a Linuxdistribution for Bioinformatics. It is easy to use, noinstallation required, CD-based distribution based onKnoppix 3.3. It includes a variety of sequence andstructure analysis packages.

URL: http://bioinformatics.org/vlinux/index.ph
http://bioknoppix.hpcf.upr.edu/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.genesdigitales.com/blastoncd/http://www.genesdigitales.com/blastoncd/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.dnalinux.com/http://www.dnalinux.com/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.vigyaancd.org/http://www.vigyaancd.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://bioknoppix.hpcf.upr.edu/http://bioknoppix.hpcf.upr.edu/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.genesdigitales.com/blastoncd/http://www.genesdigitales.com/blastoncd/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.dnalinux.com/http://www.dnalinux.com/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.vigyaancd.org/http://www.vigyaancd.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotools


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Bio-Languages:

BioJava TOP

BioJava is an open-source project dedicated toproviding a Java framework for processing biologicaldata. It include objects for manipulating sequences,file parsers, DAS client and server suport, access toBioSQL and Ensembl databases, and powerful analysisand statistical routines including a dynamicprogramming toolkit.

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

BioMOBY TOP

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

URL: http://biomoby.org/

BioPerl

TOP

Bioperl is a collection of perl modules that facilitatethe development of perl scripts for bioinformaticsapplications. As such, it does not include ready to useprograms in the sense that many commercial

packages and free web-based interfaces do (e.g.Entrez, SRS). On the other hand, bioperl does providereusable perl modules that facilitate writing perlscripts for sequence manipulation, accessing ofdatabases using a range of data formats andexecution and parsing of the results of variousmolecular biology programs including Blast, clustalw,TCoffee, genscan, ESTscan and HMMER. Consequently,

bioperl enables developing scripts that can analyzelarge quantities of sequence data in ways that aretypically difficult or impossible with web basedsystems.

URL: http://bio.perl.org/
http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.biojava.org/http://www.biojava.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://biomoby.org/http://biomoby.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://bioinformatics.org/vlinux/index.phphttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.biojava.org/http://www.biojava.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://biomoby.org/http://biomoby.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotools


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BioPipe TOP

The biopipe is a workflow framework that seeks toaddress some of the complexity involved in carryingout large scale bioinformatics analysis. It has been

designed to work intimately with the bioperl package.The main idea behind biopipe is to enable users tointegrate data from disparate sources into a commonanalysis framework. In addition, it is designed towork over a compute farm providing job managementfunctionality. This project was extended borrowingcode and concepts from the Ensembl pipeline project.

URL: http://biopipe.org/

BioPython TOP

An international association of developers of freelyavailable Python tools for computational molecularbiology. biopython.org provides an online resource formodules, scripts, and web links for developers ofPython based software for life science research.

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

BioRuby TOP

BioRuby project aims to implement an integratedenvironment for Bioinformatics with Ruby language.The BioRuby library follows the KISS principle inorder to maximize its usability and efficiency forbiologists as a daily tool.

URL: http://bioruby.org

Bio-LiveCDsProteomics:

All rights reserved rishibiotech.com. Terms and Conditions. Terms of Use.Developed and maintained by Acenet.
http://bio.perl.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://biopipe.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.biopython.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://bio.perl.org/http://bio.perl.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://biopipe.org/http://biopipe.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://www.biopython.org/http://www.biopython.org/http://www.rishibiotech.com/biotools.htm#biotools%23biotoolshttp://bioruby.org/http://www.acenetworks.com/

biosoftware links

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