BioEdit is
a biological sequence alignment editor written for Windows 95/98/NT.
A rich, intuitive multiple document interface with many convenient
features makes alignment, manipulation and viewing of sequences
relatively quick and easy on your desktop computer. Several sequence
manipulation and analysis options and fully-automated links to
local and WWW-based anaylsis programs facilitate an integrated
working environment which allows you to view, align and analyze
sequences from a single application with simple point-and-click
operations.
Welcome to
the RasMol and OpenRasMol web site. This site was established
in mid-September 2000 to provide a home for developers of Open
Source versions of RasMol. In May 2002, it also became a home
page for users of RasMol. RasMol is an important scientific tool
for visualisation of molecules created by Roger Sayle in 1992.
RasMol is used by hundreds of thousands of users world-wide to
view macromolecules and to prepare publication-quality images.
Science is best served when the tools we use are fully understood
by those who wield those tools and by those who make used of results
obtained with those tools. When a scientific tool exists as software,
access to source code is an important element in achieving full
understanding of that tool. As our field evolves and new versions
of software are required, access to source allows us to adapt
our tools quickly and effectively.
EMBOSS is "The European Molecular Biology Open Software
Suite ".
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.
Jemboss is
a java based interface to EMBOSS. It provides the advantage of
being able to provide sensible EMBOSS defaults on-the-fly for
a given sequence or for a given input parameter. Jemboss can run
the EMBOSS applications interactively or as a batch process. The
progress of the batch processes are monitored by a job manager.
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.
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. The program runs on UNIX and Windows NT/95/98/2000
and is freely available.
Bioperl is
a tookit of perl modules useful in building bioinformatics solutions
in perl. It is built in an object-oriented manner so that many
modules depend on each other to achieve a task. The collection
of modules in the bioperl-live repository consist of the core
of the functionality of bioperl. Additionally auxiliary modules
for creating graphical interfaces (bioperl-gui), persistent storage
in RDMBS (bioperl-db), running and parsing the results from hundreds
of bioinformatics applications (bioperl-run), software to automate
bioinformatic analyses (bioperl-pipeline), and CORBA bridges to
the BioCORBA (http://www.biocorba.org) specification (bioperl-corba-server
and bioperl-corba-client) are all available as CVS modules in
our repository.
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.
TreeView
provides a simple way to view the contents of a NEXUS, PHYLIP,
Hennig86, Clustal, or other format tree file. While PAUP and MacClade
have excellent tree printing facilities, there may be times you
just want to view the trees without having to load the data set
they were generated from. The PHYLIP package contains tree drawing
programs which offer a greater variety of trees than TreeView,
but are somewhat clumsy to use. The forthcoming PAUP* for Windows
does not have a graphical interface, hence TreeView allows you
to create publication quality trees from PAUP files, either directly,
or by generating graphics files for editing by other programs.
PHYLIP is a free package of programs for inferring
phylogenies. It is distributed as source code, documentation files,
and a number of different types of executables. These Web pages,
by Joe Felsenstein of the Department of Genome Sciences at the
University of Washington, contain information on PHYLIP and ways
to transfer the executables, source code and documentation to
your computer.
