The following packages are included in the present VLinux
distribution.
EMBOSS
GDE
Rasmol
PyMOL
GROMACS
Phylip
Arka/Genpak
ClustalX/ClustalW
TCoffee
Seaview
Glimmer
Mummer
Garlic
Ramachandran Plot viewer
Stride
Primer
XMolCalc
Babel
NJPlot
HMMER
Pratt
EMBOSS is a new, 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.
Within EMBOSS you will find over 100 programs (applications). These are just some of the areas covered: 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. 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, CHARMm
format, MOPAC format, CIF format and mmCIF format files. If
connectivity
information and/or secondary structure information is not contained in
the file this is calculated automatically. The loaded molecule may be
shown as wireframe, cylinder (drieding) stick bonds, alpha-carbon
trace,
spacefilling (CPK) spheres, macromolecular ribbons (either smooth
shaded
solid ribbons or parallel strands), hydrogen bonding and dot surface.
Atoms may also be labelled with arbitrary text strings. Alternate
conformers and multiple NMR models may be specially coloured and
identified in atom labels. Different parts of the molecule may be
displayed and coloured independently of the rest of the molecule or
shown in different representations simultaneously. The space filling
spheres can even be shadowed. The displayed molecule may be rotated,
translated, zoomed, z-clipped (slabbed) interactively using either the
mouse, the scroll bars, the command line or an attached dials box.
RasMol can read a prepared list of commands from a `script' file (or
via
interprocess communication) to allow a given image or viewpoint to be
restored quickly. RasMol can also create a script file containing the
commands required to regenerate the current image. Finally the rendered
image may be written out in a variety of formats including both raster
and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a
MolScript input script or Kinemage.
http://www.openrasmol.org
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.Today, PyMOL is a capable molecular viewer with
support for animations, high−quality rendering,crystallography, and
other common molecular graphics activities. It has been be adopted by
many hundreds (perhaps even thousands) of scientists spread over thirty
countries.
http://pymol.sourceforge.net
GROMACS is a package for molecular
dynamics simulation and energy minimization.
http://www.gromacs.org
PHYLIP, the Phylogeny Inference Package, is a package of programs
for inferring phylogenies (evolutionary trees). It has been distributed
since 1980, and has over 15,000 registered users, making it the most
widely distributed package of phylogeny programs. PHYLIP is available
as
source code in C, and also as executables for some common computer
systems. It can infer phylogenies by parsimony, compatibility, distance
matrix methods, and likelihood. It can also compute consensus trees,
compute distances between trees, draw trees, resample data sets by
bootstrapping or jackknifing, edit trees, and compute distance
matrices.
It can handle data that are nucleotide sequences, protein sequences,
gene frequencies, restriction sites, restriction fragments, distances,
discrete characters, and continuous characters.
http://evolution.gs.washington.edu/phylip.html
Arka is a program that serves as a graphical interface for the
programs
from the GP package (see http://bioinformatics.org/genpak/)
and
virtually for any other command line program and has some funtions on
it's own.
The main scope of the program is the manipulation and
visualisation of DNA / RNA /protein sequences
The GP package contains many command-line utilities which fullfill a
whole bunch of tasks (from DNA sequence searches to restriction
analysis and determining the melting temperature of oligonucleotides).
T-Coffee is a versatile tool for making multiple sequence
alignments. Its aim is to combine heterogeneous sources of information.
The current implementation has been especially designed for combining
local and global alignments, respectively from ClustalW and Lalign. It
can also be used to combine a series of alternative multiple sequence
alignments of the same sequences.
http://mathbio.nimr.mrc.ac.uk/~cnotred/
Seaview is a graphical multiple sequence alignment editor. SeaView
is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP,
MASE). It allows to manually edit the alignment, and also to run
DOT-PLOT or CLUSTAL programs to locally improve the alignment. It can
be
executed from the command line by typing: "seaview". It requires you to
have a running X-windows display.
Glimmer (Gene Locator and Interpolated Markov Modeler) is a system
for finding genes in microbial DNA, especially the genomes of bacteria
and archaea. It uses interpolated Markov models (IMMs) to identify the
coding regions and distinguish them from noncoding DNA. Glimmer is the
primary microbial gene finder at TIGR (The Institute for Genomic
Research), and has been used to annotate the complete genomes of B.
burgdorferi, T. pallidum, T. maritima, D. radiodurans, M. tuberculosis,
and non-TIGR projects including C. trachomatis, C. pneumoniae, and
others.The Glimmer system consists of two main programs. The first of
these is the training program, build-icm. This program takes an input
set of sequences and builds and outputs the IMM for them. These
sequences can be complete genes or just partial orfs. The second
program
is glimmer, which uses this IMM to identify putative genes in an entire
genome.
http://www.tigr.org
MUMmer is an open source software package for the rapid alignment of
very large DNA and amino acid sequences. MUMmer is a modular and
versatile package that relies on a suffix tree data structure for
efficient pattern matching. Suffix trees are suited for large data sets
because they can be constructed and searched in linear time and space.
This allows mummer to find all 20 base pair maximal exact matches
between two ~5 million base pair bacterial genomes in 20 seconds, using
90 MB of RAM, on a typical 1.7 GHz Linux desktop computer. Using a seed
and extend strategy, other parts of the MUMmer pipeline use these exact
matches as alignment anchors to generate pair-wise alignments similar
to
BLAST output. This modular design has an important side effect, it
allows for the easy reuse of MUMmer modules in other software. For
instance, one can imagine primer design, repeat masking and even
comparative annotation tools based on the efficient matching algorithm
MUMmer provides. Another advantage of MUMmer is its speed. Its low
runtime and memory requirements allow it to be used on most any
computer. MUMmer's efficiency also makes it ideal for aligning huge
sequences such as completed and draft eukarotic genomes. MUMmer has
been
successfully used to align the mouse and human genomes, showing it can
handle most any input available. In addition, its ability to handle
multiple sequences facilitate many vs. many searches, and make the
comparison of unfinished draft sequence quite simple.
http://www.tigr.org
Garlic is a free molecular viewer and editor written for unix and
unix clones. Garlic is the most portable molecular viewer in the unix
world.
http://garlic.mefos.hr/garlic
The Ramachandran Plot Explorer can be used to explore simple
conformation changes in proteins explore secondary structure (helices
and ribbons) and common loop structures construct short sequences by
mutating, deleting and adding residues
http://www.dillgroup.ucsf.edu/~bosco/index.html
Protein Secondary Structure assignment program. To get a list of possible options type 'stride --help' on a terminal without the quotes
Helps to design primers for sequences. It helps to make sure the
sequence is not a vector and not chimeric and to avoid repetitive
elements.
http://www-genome.wi.mit.edu/genome_software/other/primer3.html
A small utility that allows you to calculate a molecular weight
under Unix/X11.
http://www.oci.unizh.ch/group.pages/hesse/xmolcalc
Babel is a program to convert between various file formats. It can
be invoked using command line options or menus. The menu interface can
be accessed by typing: babel -m The command line input has the
following format:
babel [-v] -i
http://openbabel.sourceforge.net
NJplot is a tree drawing program able to draw any binary tree
expressed in the standard phylogenetic tree format (e.g., the format
used by the PHYLIP package).
ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/
HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries
Pratt allows the user to search for patterns conserved in a set of
protein sequences. The user can specify what kind of patterns should be
searched for, and how many sequences should match a pattern to be
reported.