ACT Artemis Biojava Bioperl by ccp13003

VIEWS: 98 PAGES: 10

									ACT
Website: http://www.sanger.ac.uk/Software/ACT/

Current Release: Release 4

ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. In common with Artemis, ACT is written in Java
and runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequence in
FASTA or raw format. Extra sequence features can be in EMBL, GENBANK orGFF format.

The sequence comparison displayed by ACT is usually the result of running a blastn or tblastx search. See theuser manual for more
information.

To see ACT in action go to the examples page.

To get a copy of the most recent stable release of ACT go to theRelease 4 web pages.


Artemis
Artemis is a free genome viewer and annotation tool

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: GUI
Supported Operating Systems: UNIX, GNU-Linux, Mac OS, MS-Windows
Grid Information: Information not available

DETAILS
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.

MISCELLANEOUS INFORMATION
Current Release: Version release 7
Developed by: Sanger Institute [Click here]
Medium of Development: Java
Download Size: unknown
License: free


Biojava
The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: UNIX, GNU-Linux, Mac OS, MS-Windows
Grid Information: Information not available

DETAILS
The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data. This will include objects for
manipulating sequences, file parsers, CORBA interoperability, DAS, access to ACeDB, dynamic programming, and simple statistical routines
to name just a few things. The BioJava library is useful for automating those daily and mundane bioinformatics tasks. As the library matures,
the BioJava libraries will provide a foundation upon which both free software and commercial packages can be developed.

MISCELLANEOUS INFORMATION
Current Release: Version 1.3
Developed by: The Biojava Project [Click here]
Download Size: unknown
License: free


Bioperl
The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science
research.

[Website] [Download] [Manual] [Tutorial] [Documentation]

http://bio.perl.org/Core/Latest/modules.html
IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Unix, Win9X/NT/2000, MacOSX
Grid Information: Information not available

DETAILS
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.

MISCELLANEOUS INFORMATION
Current Release: Version 1.5
Developed by: The Bioperl Project [Click here]
Download Size: unknown
License: free


Biopython
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Unix, Win9X/NT/2000, MacOSX
Grid Information: Information not available

DETAILS
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. It is a
distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in
bioinformatics. The source code is made available under extremely liberal terms, making it compatible with almost every license in the world.
We work along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project.

MISCELLANEOUS INFORMATION
Current Release: Version 1.30
Developed by: The Biopython Project [Click here]
Download Size: unknown
License: free


BLAST
Finds the degree of similarity of a given nucleotide or protein sequence against a database, also performs alignment with the sequences in
the database

[Website] [Download] [Manual] [Tutorial] [Documentation]

NEW DOCS: http://www.ncbi.nlm.nih.gov/BLAST/docs/

IMPORTANT INFORMATION
Interface: Command Line, GUI , Web [Click here]
Supported Operating Systems: Solaris, Mac, Alpha, MIPS, HPPA, x86, IA64, AIX, I
Grid Information: Yes! Can be ported to the grid.

DETAILS
Sequence alignments provide a powerful way to compare novel sequences with previously characterized genes. Both functional and
evolutionary information can be inferred from well designed queries and alignments. BLAST 2.0, (Basic Local Alignment Search Tool),
provides a method for rapid searching of nucleotide and protein databases. Since the BLAST algorithm detects local as well as global
alignments, regions of similarity embedded in otherwise unrelated proteins can be detected. Both types of similarity may provide important
clues to the function of uncharacterized proteins.

MISCELLANEOUS INFORMATION
Current Release: Version 2.2.9
Developed by: NCBI [Click here]
Medium of Development: unknown
Download Size: unknown
License: free
ClustalW
Multiple Sequence Alignment

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line, Web [Click here]
Supported Operating Systems: Unix, DOS, MacOSX, WinXP
Grid Information: Yes! Can be ported to the grid.

DETAILS
ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple
sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the
identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

MISCELLANEOUS INFORMATION
Current Release: Version 1.83
Developed by: European Bioinformatics Institute [Click here]
Download Size: unknown
License: free



Cn3D
To view 3-dimensional structures from the NCBI Entrez retrieval service

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: GUI
Supported Operating Systems: Windows, Macintosh, and Unix
Grid Information: Information not available

DETAILS
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.

MISCELLANEOUS INFORMATION
Current Release: Version 4.1
Developed by: NCBI [Click here]
Download Size: unknown
License: free




DOWSER
Surveys the structure of a protein molecule to locate internal cavities and assess the hydrophilicity of these cavities

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Information not available
Grid Information: Yes! Can be ported to the grid.

DETAILS
The program requires as input the atomic coordinates in PDB format. First, the molecular surface of internal cavities is calculated with
Connolly's MS program. Then Dowser produces as output a list giving the coordinates and the minimum energy value for placing water
molecules starting from each point on the internal surface. The positions are sorted, when two positions overlap, the one with lowest energy
is retained, and only water molecules with binding energy below -10 cal/mol are retained. The results can be viewed with programs such as
rasmol or vmd.

MISCELLANEOUS INFORMATION
Current Release: Version 3
Developed by: UNC Computational Structural Biophysics Group
Download Size: unknown
License: free
EMBOSS
European Molecular Biology Open Software Suite

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Solaris, AIX, Irix, Tru64, HPUX, Linux, MacOSX
Grid Information: Yes! Can be ported to the grid.

DETAILS
EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user
community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from
the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software
in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless
whole. EMBOSS breaks the historical trend towards commercial software packages. There are about 100 applications in this suite.

MISCELLANEOUS INFORMATION
Current Release: Version 2.8.0
Download Size: unknown
License: free


FASTA
Fast protein comparison or a fast nucleotide comparison.

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line, GUI
Supported Operating Systems: Unix, Windows, MacOSX, Linux
Grid Information: Yes! Can be ported to the grid.

DETAILS
FASTA (pronounced FAST-Aye) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide
comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised
searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word
hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity
is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not
every word hit is investigated but instead initially looks for segment's containing several nearby hits.

MISCELLANEOUS INFORMATION
Current Release: Version fasta33
Developed by: William R. Pearson, the University of Virginia
Download Size: unknown
License: free



FastDNAml
Estimating maximum likelihood phylogenetic trees from nucleotide sequences

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Unix, MacOSX, Windows
Grid Information: Information not available

DETAILS
fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the
documentation for DNAML before using this program. fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and
using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the
PHYLIP 3.3 DNAML program from PASCAL to C.

MISCELLANEOUS INFORMATION
Current Release: Version 1.2.2
Developed by: Don Berry, Indiana Univerisity, Gary Olsen, UIUC
Download Size: unknown
License: free
GlimmerM
A gene finder derived from Glimmer, but developed specifically for eukaryotes.

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line, Web [Click here]
Supported Operating Systems: Linux RedHat 6.x+, Sun Solaris, and Alpha OSF1
Grid Information: Information not available

DETAILS
A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programing 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). The system has been trained for Arabidopsis thaliana, Oryza sativa (rice), and Plasmodium falciparum (the malaria parasite), and
should work well on closely related organisms.

MISCELLANEOUS INFORMATION
Current Release: Version 2.5.1
Developed by: The Institute for Genomic Research [Click here]
Download Size: unknown
License: free


GROMACS
GROMACS is a versatile package to perform molecular dynamics for systems with hundreds to millions of particles.

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Unix, Linux
Grid Information: Information not available

DETAILS
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.

MISCELLANEOUS INFORMATION
Current Release: Version 3.2
Developed by: Herman Berendsens group, Groningen University
Download Size: unknown
License: free


HMMER
Sequence Analysis using profile Hidden Markov Models

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Unix, MacOSX, Linux
Grid Information: Yes! Can be ported to the grid.

DETAILS
Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence
family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. Basically, you
give HMMER a multiple sequence alignment as input; it builds a statistical model called a "hidden Markov model" which you can then use as
a query into a sequence database to find (and/or align) additional homologues of the sequence family.

MISCELLANEOUS INFORMATION
Current Release: Version 2.3.2
Developed by: School of Medicine,Washington University,St. Loui
Download Size: unknown
License: free
Image
Package of analysis algorithms for processing gel images

[Website] [Download] [Manual] [Tutorial] [Documentation]

Online Help: http://www.sanger.ac.uk/Software/Image/imhelp/

Online Tutorial: http://www.sanger.ac.uk/Software/Image/tutorial/

IMPORTANT INFORMATION
Interface: GUI
Supported Operating Systems: Alpha, Linux (6.2 and 7.1), SGI, Solaris
Grid Information: Information not available

DETAILS
Image is a package of analysis algorithms for processing gel images from restriction digest fingerprinting experiments. Image provides a
robust tool for large scale physical mapping. Image is able to process gels from a wide variety of scanning technologies and has been tested
on various fingerprinting protocols, producing normalized band and gel images as output. The gel image is scanned or otherwise imported as
an image file, and analyzed step by step. At each step the gel is analyzed a little further, and the results are displayed on the screen, where a
manual editor is provided at each stage.

MISCELLANEOUS INFORMATION
Current Release: Version 3.10b
Developed by: Fred Wobus and Darren Platt
Download Size: unknown
License: free


LOOPP
Learning, Observing and Outputting Protein Patterns

[Website] [Download] [Manual] [Tutorial] [Documentation]

Online Tutorial: http://cbsu.tc.cornell.edu/software/loopp/loopp_doc.html

IMPORTANT INFORMATION
Interface: Command Line, Web [Click here]
Supported Operating Systems: IBM RS/6000 and SP, WinNT/2K, SGI, Solaris, Linux
Grid Information: Yes! Can be ported to the grid.

DETAILS
LOOP(Learning, Observing and Outputting Protein Patterns) is a program for potential optimization and alignments. LOOPP aligns sequence
to sequence, sequence to structure, and structure to structure. It further enables the optimization of potentials and scoring functions for the
above mentioned applications.

MISCELLANEOUS INFORMATION
Current Release: Version 2
Developed by: Jarek Meller and Ron Elber, Cornell [Click here]
Download Size: unknown
License: free



Mapmaker/QTL
MAPMAKER/QTL is a program for mapping genes.

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: DOS, Solaris
Grid Information: Yes! Can be ported to the grid.

DETAILS
MAPMAKER/QTL is a program for mapping these genes using the techniques of "interval mapping" and "simultaneous search". Interval
mapping uses the power of a complete genetic map to discern weak effects from genetic distance between marker locus and putative QTL
(Quantitative Trait Locus), while "simultaneous search" allows us to fit multiple QTLs across the genome at once, thus reducing the overall
non- genetic variance in the trait. Both techniques together provide increased "power" for detecting QTLs, allowing one to find genes with
smaller effects (in equivalent data sets) than one can using simpler phenotype on genotype correlations.

MISCELLANEOUS INFORMATION
Current Release: Version 1.1
Developed by: Leonid Kruglyak, Mark Daly [Click here]
Download Size: unknown
License: free


NAB
A Computer Language for Structural Exploration

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Linux, Mac OsX, Solaris, UNIX, Windows
Grid Information: Yes! Can be ported to the grid.

DETAILS
NAB was originally designed as a small modeling language (a "molecular awk"), with a principal focus on constructing models for non-helical
nucleic acids. It has been used to construct models of helical and non-helical nucleic acids from a few dozen to a few hundred nucleotides in
size, and provides a combination of rigid body transformations and distance geometry to create candidate structures that match input criteria.
We have applied NAB to duplex-, triplex- and tetraplex DNA, to RNA hairpins and pseudo-knots, to closed-circular DNA, and to models of
the small subunit of the ribosome and of recombination sites.

MISCELLANEOUS INFORMATION
Current Release: Version 5.1.2
Developed by: David A. Case, The Scripps Research Institute [Click here]
Download Size: unknown
License: free



NAMD
High-performance simulation of large biomolecular systems

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: AIX, IBM-SP, HPUX, Linux, Solaris, Tru64, Windows
Grid Information: Yes! Can be ported to the grid.

DETAILS
The structures of increasingly larger biomolecular aggregates are being determined. 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
switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code.

MISCELLANEOUS INFORMATION
Current Release: Version 2.5
Developed by: Theoretical & Computational Biophysics Group, UIUC [Click here]
Download Size: unknown
License: free


NMRView
Visualization and Analysis of Nuclear Magnetic Resonance Data

[Website] [Download] [Manual] [Tutorial] [Documentation]

ONLINE MANUAL: http://onemoonscientific.com/nmrview/manual/index.html



IMPORTANT INFORMATION
Interface: GUI
Supported Operating Systems: Solaris, SGI, Linux (x86 & PowerPC), Java platform
Grid Information: No! Cannot be ported to the grid.

DETAILS
NMRView is a program for the visualization and analysis of processed NMR data. It is intended to be able to do everything from the
processed data to the input for structure generation programs. NMRView contains features that allow for processing of data, but these
features are new and should be considered experimental.
MISCELLANEOUS INFORMATION
Current Release: Version 6.2.9
Developed by: Bruce A. Johnson, Merck Research Laboratories
Download Size: unknown
License: free


PAML
Phylogenetic analyses of DNA or protein sequences using maximum likelihood

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Unix, Linux, MacOSX, Windows
Grid Information: Yes! Can be ported to the grid.

DETAILS
* Estimation of branch lengths in a phylogenetic tree and parameters in the evolutionary model such as the transition/transversion rate ratio,
the shape parameter of the gamma distribution for variable evolutionary rates among sites, and rate parameters for different genes; Test of
hypotheses concerning sequence evolution, such as rate constancy and independence among nucleotide or amino acid sites, rate constancy
among lineages (the molecular clock), and homogeneity of evolutionary process in multiple genes; * Calculation of substitution rates at sites;
* Reconstruction of ancestral nucleotide or amino acid sequences; * Simulation of nucleotide, codon, and amino acid sequence data sets; *
Calculation of substitution rates at sites; * Reconstruction of ancestral nucleotide or amino acid sequences; * Simulation of nucleotide, codon,
and amino acid sequence data sets

MISCELLANEOUS INFORMATION
Current Release: Version 3.14
Developed by: Ziheng Yang, University College London [Click here]
Download Size: unknown
License: free


PHYLIP
A free package of programs for inferring phylogenies

[Website] [Download] [Manual] [Tutorial] [Documentation]

Online Documentation: http://evolution.genetics.washington.edu/phylip/phylip.html

IMPORTANT INFORMATION
Interface: Command Line, Web [Click here]
Supported Operating Systems: Solaris, HPUX, SGI, DEC, Windows, Linux, Mac
Grid Information: Yes! Can be ported to the grid.

DETAILS
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are
available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data
types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.

MISCELLANEOUS INFORMATION
Current Release: Version 3.63
Developed by: Joe Felsenstein, Dept. of Genome Sciences, U.Wash
Download Size: unknown
License: free


RasMol
Molecular Graphics Visualization Tool

[Website] [Download] [Manual] [Tutorial] [Documentation]

Online Documentation: http://www.umass.edu/microbio/rasmol/rasras.htm

IMPORTANT INFORMATION
Interface: GUI
Supported Operating Systems: Solaris, HPUX, IRIX, OpenVMS
Grid Information: No! Cannot be ported to the grid.

DETAILS
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.
MISCELLANEOUS INFORMATION
Current Release: Version 2.7.2.1
Developed by: Univerisity of Massachusetts [Click here]
Download Size: unknown
License: free


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

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line, GUI , Web
Supported Operating Systems: Unix, Windows, MacOSX, Linux
Grid Information: Yes! Can be ported to the grid.

DETAILS
readseq is a reformatting program for DNA or protein sequence data developed by Don Gilbert. It allows the input of single or multiple
sequences in 18 different formats and converts to a specified format.

MISCELLANEOUS INFORMATION
Current Release: Version 2
Developed by: Don Gilbert, University of Indiana
Medium of Development: Java
Download Size: unknown
License: free


T-Coffee
Multiple Sequence Alignments

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line, GUI , Web [Click here]
Supported Operating Systems: Unix, MS-DOS, MacOSX
Grid Information: Yes! Can be ported to the grid.

DETAILS
T-Coffee is more accurate than ClustalW for sequences with less than 30% identity, but it is slower. The method is broadly based on the
popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-
Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information
that can be used to guide the progressive alignment.

MISCELLANEOUS INFORMATION
Current Release: Version 1.37
Developed by: Notredame, Higgins, Heringa
Download Size: unknown
License: free


TribeMCL
An efficient algorithm for large-scale detection of protein families

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Unix, Linux
Grid Information: No! Cannot be ported to the grid.

DETAILS
TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'. This clustering is achieved by analysing
similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into related groups. In many cases,
proteins in the same protein familywill have similar functional properties. TribeMCL uses a novel clustering method (Markov Clustering or
MCL) which solves problems which normally hinder protein sequence clustering. These problems include: multi-domain proteins, peptide
fragments and proteins which possess domains which are very widespread (promiscuous domains). The efficiency of the method makes it
applicable to the clustering of very large datasets. We routinely use the algorithm to cluster datasets as large as 500,000 peptides.

MISCELLANEOUS INFORMATION
Current Release: Version Mcl-03-276
Developed by: Enright A.J., Van Dongen S., Ouzounis C.A
Download Size: unknown
License: free


VMD
Molecular visualization program for displaying, animating, and analyzing large biomolecular systems

[Website] [Download] [Manual] [Tutorial] [Documentation]

ONLINE TUTORIAL: http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html

IMPORTANT INFORMATION
Interface: GUI
Supported Operating Systems: Unix, MacOSX, Windows
Grid Information: No! Cannot be ported to the grid.

DETAILS
List of VMD features * General Molecular Visualisation * Visualisation of dynamic molecular data * Interactive molecular dynamics
simulations * Molecular analysis commands * Tcl and Python scripting languages * Support for multimodal input and various display systems
* Easy to Extend

MISCELLANEOUS INFORMATION
Current Release: Version 1.8.3
Developed by: Theoretical & Computational Biophysics Group, UIUC [Click here]
Download Size: unknown
License: free


Wise2
Comparisons of DNA sequence and protein sequence.

[Website] [Download] [Manual] [Tutorial] [Documentation]

IMPORTANT INFORMATION
Interface: Command Line
Supported Operating Systems: Unix, Linux
Grid Information: Yes! Can be ported to the grid.

DETAILS
Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

MISCELLANEOUS INFORMATION
Current Release: Version 2.1.20
Developed by: Ewan Birney, Richard Copley, EBI [Click here]
Download Size: unknown
License: free

								
To top