VigyaanCD.org header image
 

Biology software included

Software Description Links
Artemis DNA sequence viewer and annotation tool. More Online Manual
FAQs
Examples
Bioperl Perl tools for computational molecular biology. More Tutorial
FAQs
ClustalX Interactive program for multiple sequence alignment. Friendly GUI. More Home page
Cn3D Structure visualizer for NCBI's Entrez retrieval service. More Tutorial
EMBOSS tools A suite of program for sequence and pattern alignment, protein motif identification and more. More Tutorial
Garlic Interactive program for molecular visualization. Friendly GUI. More Documentation
Glimmer Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. More
GROMACS Suite of programs for molecular dynamics and more. More Online Manual
Tutorials
FAQs
GP/Arka Programs for manipulation of DNA/RNA/protein sequences. More
MUMmer MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. More Manual
NCBI tools Bioinformatics tools from NCBI. More
NJPlot A binary tree drawing program for phylogenetic trees. More Online Help
Example tree file
Open Babel Converts between different file formats for computational biology applications More Formats
FAQs
PyMOL Molecular visualization program with high quality image output. More Manuals
FAQs
Useful scripts
Ramachandran Plot Explorer Protein visualizer More Home page
Rasmol Molecular visualization program More Home page
Raster3D Program for high quality image output for biomolecules. More FAQs
Online docs
Sample figures
SeaView SeaView is a graphical multiple sequence alignment More Reference
Example data file
Online help
TINKER Software tools for molecular modeling (MD). More Online Guide


Artemis

Homepage: http://www.sanger.ac.uk/Software/Artemis/
Version: Release 6 License: GPL
Description: Description: 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. It can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format.
Online Manual
FAQs
Examples

Bioperl

Homepage: http://www.bioperl.org/
Version: 1.4 License: Artisitc
Description: The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules.
Tutorial
FAQs

ClustalX

Homepage: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html
Version: 1.83 License: click here
Description: Clustal X is a graphical interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment.

User can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.

Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted.

Cn3D

Homepage: http://www.ncbi.nih.gov/Structure/CN3D/cn3d.shtml
Version: 3.0 License: Click here
Description: Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.
Tutorial

EMBOSS

Homepage: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
Version: 2.10.0 License: GPL
Description: Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered:
  • Sequence alignment
  • Rapid database searching with sequence patterns
  • Protein motif identification, including domain analysis
  • Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats.
  • Codon usage analysis for small genomes
  • Rapid identification of sequence patterns in large scale sequence sets.
  • Presentation tools for publication
  • And much more.
Tutorial

Garlic

Homepage: http://garlic.mefos.hr/garlic/
Version: 1.4 License: GPL
Description: Garlic is a molecular visualization program. It's written for the investigation of membrane proteins. It may be used to visualize other proteins, as well as some geometric objects. The included version of garlic recognizes PDB format version 2.1. Garlic may also be used to analyze protein sequences.
Documentation

Ghemical

Homepage: http://www.uku.fi/~thassine/ghemical/
Version: 1.01License: GPL
Description: Ghemical a very versatile simulation engine for molecular modeling and quantum-mechanical calculations. Its friendly GUI is suitable for beginners.

Glimmer

Homepage: http://www.tigr.org/software/glimmer/
Version: 2.13 License: Artistic
Description: Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. Glimmer use 3-periodic nonhomogenous Markov models in their IMMs.

GROMACS

Homepage: http://www.gromacs.org/
Version: 3.2.1 License: GPL
Description: 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.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Online Manual
Tutorials
FAQs

GP/Arka

Homepage: http://bioinformatics.org/genpak/index.html
Version: GP 0.26, Arka 0.11 License: GPL
Description: GP and Arka are very leightweighed programs for manipulation of DNA/RNA/protein sequences. They are designed on one hand to run smoothly on older machines, and on the other -- to faciliate processing of large numbers of sequence/data files. GP includes utilities to convert DNA/RNA to protein, determine codon usage/GC contents, promotor searches, Tm, searching for restriction sites, converting sequences into numerical representations and much more.

GP is 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.

Arka is a program that serves as a graphical interface for the programs from the GP package.

MUMmer

Homepage: http://www.tigr.org/software/mummer/
Version: 3.15 License: Artistic
Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
Manual


NCBI Toolkit

Reference Web-site: http://www.ncbi.nlm.nih.gov/BLAST/
Version: 6.1.20041020-2 License: Click here
Description: The NCBI (National Center for Biotechnology Information) Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.

NJPlot

Homepage: http://pbil.univ-lyon1.fr/software/njplot.html
Version: 0.20030331-1 License: Artistic
Description: NJplot is able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the Phylip package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Online Help
Example tree file


Open Babel

Homepage: http://openbabel.sourceforge.net/
Version: 1.100.2 License: GPL
Description: Open Babel is a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
List of supported file formats
FAQs


PyMOL

Homepage: http://pymol.sourceforge.net/
Version: 0.97 License: click here
Description: 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. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
Manuals
FAQs
Useful scripts

The Ramachandran Plot Explorer

Homepage: http://www.dillgroup.ucsf.edu/~bosco/rama.html
Version: 0.9 License: GPL
Description: The Ramachandran Plot Explorer really does offer something new. It has been specially designed to focus solely on the phi, psi and chi angles. It can also easily:
explore conformation changes
explore secondary structure and common loop structures
construct and edit protein sequences interactively

Rasmol

Homepage: http://www.umass.edu/microbio/rasmol/index2.htm
Version: 2.7.2.1.1 License: click here
Description: RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program has been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structure Department at Glaxo Research and Development, Greenford, UK.

RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations.

Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XMol XYZ format and CHARMm format files. If connectivity information and/or secondary structure information is not contained in the file this is calculated automatically.

Raster3D

Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html
Version: 2.7c License: Binaries only for VigyaanCD
Description: 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. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.
FAQs
Online documentation
Sample figures

SeaView

Homepage: http://pbil.univ-lyon1.fr/software/seaview.html
License: GPL
Description: SeaView is a graphical multiple sequence alignment editor developed by Manolo Gouy. SeaView 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.
Reference
Example data file
Online help

TINKER

Homepage: http://dasher.wustl.edu/tinker/
Version: 4.2 License: Binaries only for VigyaanCD
Important Note: TINKER version included on VigyaanCD should be considered as a trial version. Users planning to use TINKER on a regular basis, should obtain a copy from the TINKER homepage and are also requested to register their copy.
Description: The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L). Parameter sets for other standard force fields such as UFF, ENCAD and MM4 are under consideration. In addition, we are actively developing our own AMOEBA force field based upon polarizable atomic multipole electrostatics.
The TINKER package includes a variety of novel algorithms such as a new distance geometry metrization method that has greater speed and better sampling than standard methods, Elber's reaction path methods, several of our Potential Smoothing and Search (PSS) methods for global optimization, an efficient potential surface scanning procedure, a flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, a selection of continuum solvation treatments including several variants of the generalized Born (GB/SA) model, an efficient truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, velocity Verlet stochastic dynamics, an improved spherical energy cutoff method, Particle Mesh Ewald summation for partial charges and regular Ewald for polarizable multipoles, a novel reaction field treatment of long range electrostatics, and more....
Note: The doc, examples and params directories of TINKER are available on VigyaanCD in the directory:
/usr/local/share/tinker


Home | Downloads | Biology Tools | Chemistry Tools | Other Tools | Screenshots | Links

This page is hosted by Oak Ridge National Laboratory, USA | ccs/cbi | csm -- disclaimer
Content owner: Pratul K. Agarwal, agarwalpk_AT_ornl.gov
URL http://www.vigyaanCD.org/bio.html
Updated: Thursday, 21-Apr-2005 10:16:42 EDT
webmaster