|
Danh sách phần mềm sắp
xếp theo chủ đề
(nguồn
bioinformatics.org)
|
PyMol |
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. |
|
autoseq |
a small package of
base calling software
for ABI automated DNA
sequencers |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
phred |
Phred reads DNA
sequencer trace data,
calls bases, assigns
quality values to the
bases, and writes the
base calls and quality
values to output files. |
|
Staden Package |
This is a free to
academics (charge for
commercial users)
package including
sequence assemble, trace
viewing/editing and
sequence analysis tools.
It also includes a GUI
to the free EMBOSS
suite. |
|
autoseq |
a small package of
base calling software
for ABI automated DNA
sequencers |
|
JAligner |
JAligner is a Java
implementation of
biological sequence
alignment algorithms. |
|
Blixem |
Blixem, which stands
for "BLast matches In an
X-windows Embedded
Multiple alignment", is
an interactive browser
of pairwise Blast
matches that have been
stacked up in a
"master-slave" multiple
alignment. |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
clustalw |
The famous ClustalW
multiple alignment
program |
|
clustalx |
Clustal X provides a
window-based user
interface to the
ClustalW multiple
alignment program |
|
DCSE |
DCSE (Dedicated
Comparative Sequence
Editor) is a multiple
alignment editor |
|
Deep View
Swiss-PdbViewer |
Swiss-PdbViewer is
an application that
provides a user friendly
interface allowing to
analyse several proteins
at the same time |
|
DIALIGN |
DIALIGN is an
alignment program that
relies on comparison of
whole segments of the
sequences instead of
comparison of single
residue |
|
gBioSeq |
Biological sequence
(ADN, protein) editor
for GTK/Linux |
|
JAligner |
JAligner is a Java
implementation of
biological sequence
alignment algorithms. |
|
Jalview |
Jalview - a java
multiple alignment
editor |
|
Mauve |
Mauve is a multiple
genome alignment and
visualization package
that considers
large-scale
rearrangements in
addition to nucleotide
substitution and indels. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
Musca |
Multiple sequence
alignment of aa or
nucleotide sequences /
uses pattern discovery |
|
MUSCLE |
Multiple sequence
alignment. More accurate
than T-Coffee, faster
than CLUSTALW. |
|
PhyloDraw |
PhyloDraw is a
drawing tool for
creating phylogenetic
trees. PhyloDraw
supports various kinds
of multialignment
programs (Dialign2,
Clustal-W, Phylip
format, and pairwise
distance matrix) and
visualizes various kinds
of tree diagrams, e.g.
rectangular cl |
|
SAM equence Alignment
and Modeling Syste |
a collection of
flexible software tools
for creating, refining,
and using linear hidden
Markov models for
biological sequence
analysis |
|
seaview |
SeaView is a
graphical multiple
sequence alignment
editor |
|
ShadyBox. |
ShadyBox. The FIRST
GUI based WYSIWYG
multiple sequence
alignment drawing
program for Major Unix
platforms |
|
xsact |
EST clustering tool |
|
DCSE |
DCSE (Dedicated
Comparative Sequence
Editor) is a multiple
alignment editor |
|
gBioSeq |
Biological sequence
(ADN, protein) editor
for GTK/Linux |
|
Jalview |
Jalview - a java
multiple alignment
editor |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
seaview |
SeaView is a
graphical multiple
sequence alignment
editor
|
|
DIALIGN |
DIALIGN is an
alignment program that
relies on comparison of
whole segments of the
sequences instead of
comparison of single
residue |
|
Blixem |
Blixem, which stands
for "BLast matches In an
X-windows Embedded
Multiple alignment", is
an interactive browser
of pairwise Blast
matches that have been
stacked up in a
"master-slave" multiple
alignment. |
|
Amplicon |
Program for
designing group-specific
PCR primer sets |
|
ARB |
Microbiologist's
sequence database tool |
|
BioJava |
The BioJava Project
is an open-source
project dedicated to
providing Java tools for
processing biological
data. |
|
Biopython |
The Biopython
Project is an
international
association of
developers of freely
available Python tools
for computational
molecular biology. |
|
BioWish |
Biowish is a
C-extension for the
Tcl/Tk scripting
language |
|
Blast |
BLAST (Basic Local
Alignment Search Tool)
is a set of similarity
search programs designed
to explore all of the
available sequence
databases |
|
caRNAc |
RNA secondary
structure inference for
set of homologous
sequences |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
clustalw |
The famous ClustalW
multiple alignment
program |
|
clustalx |
Clustal X provides a
window-based user
interface to the
ClustalW multiple
alignment program |
|
CNS |
The 'Crystallography
& NMR System' for
macromolecular structure
anaylsis |
|
DNA-GUI |
DNA Graphical User
Interface |
|
EMBOSS |
EMBOSS is a package
of high-quality FREE
Open Source software for
sequence analysis. |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
MAExplorer |
The Microarray
Explorer (MAExplorer) is
a Java-based data-mining
facility for microarray
databases run as a
stand-alone program. It
includes graphics,
statistics, clustering,
reports, data filtering. |
|
MPSRCH |
MPSRCH (tm) is a
suite of Smith-Waterman
sequence analysis
programs which run under
Linux and Tru64 on Intel
and Alpha. |
|
NCRNASCAN |
a structural RNA
genefinder |
|
PatScan |
PatScan is a pattern
matcher which searches
protein or nucleotide
(DNA, RNA, tRNA etc.)
sequence archives for
instances of a pattern
which you input |
|
PKNOTS |
RNA pseudoknot
prediction |
|
Pratt |
a pattern discovery
tool |
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
readseq |
Reads and writes
nucleic/protein
sequences in various
format |
|
SEALS |
SEALS (A System for
Easy Analysis of Lots of
Sequences) is a software
package expressly
designed for large-scale
research projects in
bioinformatics. |
|
sp2fasta |
produce a file in
FASTA format from one in
SWISSPROTor EMBL flat
file format |
|
Staden Package |
This is a free to
academics (charge for
commercial users)
package including
sequence assemble, trace
viewing/editing and
sequence analysis tools.
It also includes a GUI
to the free EMBOSS
suite. |
|
Teiresias-based
Association Discovery |
Discover
associations in your
data set (gene
expression analysis,
phenotype analysis,
etc.) |
|
Teiresias-based Gene
expression analysis |
Discover patterns in
microarray data using
the Teiresias algorithm.
Allows discovery of
inversely regulated
genes. |
|
Toucan |
A Java tool for
regulatory sequence
analysis: detecting
over-represented motifs
and modules in sets of
co-regulated genes. |
|
TREE-PUZZLE: |
TREE-PUZZLE: Maximum
likelihood analysis for
nucleotide, amino acid,
and two-state data |
|
tRNAscan-SE |
tRNA detection in
genome sequences,
detects ~99% of
eukaryotic nuclear or
prokaryotic tRNA genes,
with a false positive
rate of less than one
per 15 gigabases, and
with a search speed of
about 30 kb/second. |
|
UltraScan |
UltraScan is a
comprehensive GUI
editing and data
analysis package for
hydrodynamic data from
analytical
ultracentrifugation
experiments |
|
VEGA |
VEGA was developed
to create a bridge
between most of the
molecular software
packages, like BioDock,
Quanta/CHARMm, Insight
II, MoPac, etc. In this
tool have been also
implemented some
features that are useful
to analyze, display and
manage the 3D struct |
|
WU-Blast |
Washington U. Blast |
|
UltraScan |
UltraScan is a
comprehensive GUI
editing and data
analysis package for
hydrodynamic data from
analytical
ultracentrifugation
experiments |
|
MPSRCH |
MPSRCH (tm) is a
suite of Smith-Waterman
sequence analysis
programs which run under
Linux and Tru64 on Intel
and Alpha. |
|
consed |
A Unix-based
Graphical Editor and
Automated Finishing
Program for Phrap
Sequence Assemblies |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
Staden Package |
This is a free to
academics (charge for
commercial users)
package including
sequence assemble, trace
viewing/editing and
sequence analysis tools.
It also includes a GUI
to the free EMBOSS
suite. |
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
autoseq |
a small package of
base calling software
for ABI automated DNA
sequencers |
|
phred |
Phred reads DNA
sequencer trace data,
calls bases, assigns
quality values to the
bases, and writes the
base calls and quality
values to output files. |
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
NAMD |
NAMD is a parallel,
object-oriented
molecular dynamics code
designed for
high-performance
simulation of large
biomolecular systems.
|
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
Garlic |
a free molecular
visualization program |
|
SeqPup |
SeqPup biological
sequence editor and
analysis program |
|
Biogrep |
A grep that is
optimized for
biosequences. Biogrep is
designed to locate large
sets of patterns in
sequence databases in
parallel. |
|
Blixem |
Blixem, which stands
for "BLast matches In an
X-windows Embedded
Multiple alignment", is
an interactive browser
of pairwise Blast
matches that have been
stacked up in a
"master-slave" multiple
alignment. |
|
DBWatcher |
DBWatcher is a
program handling
periodic BLAST searches
to find similarities to
your own sequences. |
|
mpiBLAST |
mpiBLAST is a
parallel implementation
of NCBI-BLAST that uses
database segmentation.
It achieves a
super-linear speedup in
some cases. |
|
MSPcrunch |
a BLAST enhancement
filter |
|
WU-Blast |
Washington U. Blast |
|
Blixem |
Blixem, which stands
for "BLast matches In an
X-windows Embedded
Multiple alignment", is
an interactive browser
of pairwise Blast
matches that have been
stacked up in a
"master-slave" multiple
alignment. |
|
MSPcrunch |
a BLAST enhancement
filter |
|
Spock |
a full-featured
molecular graphics
program |
|
Angler |
A Browser of
C.elegans Embryo
Development In Time and
Space |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
Kintecus |
Run chemical
kinetics/fitting of
catalyst reactor, and
enzyme reactions |
|
MOPAC7 |
a general-purpose
semi-empirical molecular
orbital package for the
study of chemical
structures and
reactions. |
|
io_lib |
An open source C
library of sequence
trace files supporting
ABI, ALF, SCF, CTF and
ZTR file formats. |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
phred |
Phred reads DNA
sequencer trace data,
calls bases, assigns
quality values to the
bases, and writes the
base calls and quality
values to output files. |
|
Sight |
Allows programming
free assembling of web
resoureces, local
executables and ssh
services into arbitrary
workflow. |
|
caRNAc |
RNA secondary
structure inference for
set of homologous
sequences |
|
GenomePixelizer |
Genome Visualization
Tool: Detection of
duplicating events in
genomes, Displaying the
Genetic Maps,
Comparative genetics in
general. |
|
RNA GENiE |
A web based program
for the prediction of
rna genes in genomic DNA
sequences |
|
GenomeInspector |
Software for the
analysis of spatial
correlations of elements
on DNA sequences |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
CNS |
The 'Crystallography
& NMR System' for
macromolecular structure
anaylsis |
|
UltraScan |
UltraScan is a
comprehensive GUI
editing and data
analysis package for
hydrodynamic data from
analytical
ultracentrifugation
experiments |
|
Sight |
Allows programming
free assembling of web
resoureces, local
executables and ssh
services into arbitrary
workflow. |
|
Acedb |
Acedb is a genome
database system
originally developed for
the C.elegans genome
project |
|
ARB |
Microbiologist's
sequence database tool |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
HMMER |
Profile hidden
Markov models for
biological sequence
analysis |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
mpiBLAST |
mpiBLAST is a
parallel implementation
of NCBI-BLAST that uses
database segmentation.
It achieves a
super-linear speedup in
some cases. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
HMMER |
Profile hidden
Markov models for
biological sequence
analysis
|
|
mpiBLAST |
mpiBLAST is a
parallel implementation
of NCBI-BLAST that uses
database segmentation.
It achieves a
super-linear speedup in
some cases. |
|
MeltSim |
Calculation of DNA
melting curves and maps
using the
Poland-Scheraga
algorithm and empirical
constraints by R.D.
Blake. |
|
Leksbot |
an explanatory
dictionary of botanic
and biological terms |
|
GenomeInspector |
Software for the
analysis of spatial
correlations of elements
on DNA sequences |
|
MeltSim |
Calculation of DNA
melting curves and maps
using the
Poland-Scheraga
algorithm and empirical
constraints by R.D.
Blake. |
|
Artemis |
a DNA sequence
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. |
|
consed |
A Unix-based
Graphical Editor and
Automated Finishing
Program for Phrap
Sequence Assemblies |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
phred |
Phred reads DNA
sequencer trace data,
calls bases, assigns
quality values to the
bases, and writes the
base calls and quality
values to output files. |
|
Garlic |
a free molecular
visualization program |
|
PhyloDraw |
PhyloDraw is a
drawing tool for
creating phylogenetic
trees. PhyloDraw
supports various kinds
of multialignment
programs (Dialign2,
Clustal-W, Phylip
format, and pairwise
distance matrix) and
visualizes various kinds
of tree diagrams, e.g.
rectangular cl |
|
ShadyBox. |
ShadyBox. The FIRST
GUI based WYSIWYG
multiple sequence
alignment drawing
program for Major Unix
platforms |
|
GEANFAMMER |
GEnome ANalysis and
Protein FAMily MakER |
|
GenomePixelizer |
Genome Visualization
Tool: Detection of
duplicating events in
genomes, Displaying the
Genetic Maps,
Comparative genetics in
general. |
|
PhyloGrapher |
PhyloGrapher is a
program designed to
visualize and study
evolutional relationship
between families of
homologous genes or
proteins. PhyloGrapher
is a drawing tool that
generates custom graphs
out of the given set of
genes based on distance
matrix file. |
|
PhyloGrapher |
PhyloGrapher is a
program designed to
visualize and study
evolutional relationship
between families of
homologous genes or
proteins. PhyloGrapher
is a drawing tool that
generates custom graphs
out of the given set of
genes based on distance
matrix file. |
|
Deep View
Swiss-PdbViewer |
Swiss-PdbViewer is
an application that
provides a user friendly
interface allowing to
analyse several proteins
at the same time |
|
consed |
A Unix-based
Graphical Editor and
Automated Finishing
Program for Phrap
Sequence Assemblies |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
sp2fasta |
produce a file in
FASTA format from one in
SWISSPROTor EMBL flat
file format |
|
Staden Package |
This is a free to
academics (charge for
commercial users)
package including
sequence assemble, trace
viewing/editing and
sequence analysis tools.
It also includes a GUI
to the free EMBOSS
suite. |
|
Staden Package |
This is a free to
academics (charge for
commercial users)
package including
sequence assemble, trace
viewing/editing and
sequence analysis tools.
It also includes a GUI
to the free EMBOSS
suite. |
|
SEPON |
SEPON designs
gene-specific
oligonucleotides for
microarray experiments
and is able to use EST
input from organisms in
which the genome is not
annotated for genes.
SEPON implements a novel
algorithm for reducing
cross-hybridization by
utilizing thermodyna |
|
xsact |
EST clustering tool |
|
xsact |
EST clustering tool |
|
GRS |
A Graphic Tool for
Genome Retrieval and
Segment Analysis |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
GenomePixelizer |
Genome Visualization
Tool: Detection of
duplicating events in
genomes, Displaying the
Genetic Maps,
Comparative genetics in
general. |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
GenomePixelizer |
Genome Visualization
Tool: Detection of
duplicating events in
genomes, Displaying the
Genetic Maps,
Comparative genetics in
general. |
|
Abacus |
ABaCUS is a
no-frills program
developed to investigate
the significance of the
putative correspondence
between exons and units
of protein structure. |
|
BioWish |
Biowish is a
C-extension for the
Tcl/Tk scripting
language |
|
VEGA |
VEGA was developed
to create a bridge
between most of the
molecular software
packages, like BioDock,
Quanta/CHARMm, Insight
II, MoPac, etc. In this
tool have been also
implemented some
features that are useful
to analyze, display and
manage the 3D struct |
|
UltraScan |
UltraScan is a
comprehensive GUI
editing and data
analysis package for
hydrodynamic data from
analytical
ultracentrifugation
experiments |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
Babel |
a program designed
to interconvert a number
of file formats
currently used in
molecular modeling |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
GEANFAMMER |
GEnome ANalysis and
Protein FAMily MakER |
|
MAExplorer |
The Microarray
Explorer (MAExplorer) is
a Java-based data-mining
facility for microarray
databases run as a
stand-alone program. It
includes graphics,
statistics, clustering,
reports, data filtering. |
|
Teiresias-based
Association Discovery |
Discover
associations in your
data set (gene
expression analysis,
phenotype analysis,
etc.) |
|
VEIL |
A hidden Markov
model for finding genes
in vertebrate DNA? |
|
Toucan |
A Java tool for
regulatory sequence
analysis: detecting
over-represented motifs
and modules in sets of
co-regulated genes. |
|
SEPON |
SEPON designs
gene-specific
oligonucleotides for
microarray experiments
and is able to use EST
input from organisms in
which the genome is not
annotated for genes.
SEPON implements a novel
algorithm for reducing
cross-hybridization by
utilizing thermodyna |
|
geneid |
Gene prediction
tool, it can also
introduce homology and
annotation evidences and
produce a reannotation
of a genomic sequence. A
pthreads parallel
version also available. |
|
geneid |
Gene prediction
tool, it can also
introduce homology and
annotation evidences and
produce a reannotation
of a genomic sequence. A
pthreads parallel
version also available. |
|
Populations |
Population genetic
software (individuals or
populations distances,
phylogenetic trees) |
|
Artemis |
a DNA sequence
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. |
|
Ensembl |
software system
which produces and
maintains automatic
annotation on
eukaryoticgenomes |
|
On-line Genome
Annotations |
Annotations for many
eukaryotic, bacterial
and archaeal genomes.
Can be searched using
accession numbers or
sought features |
|
On-line Genome
Annotations |
Annotations for many
eukaryotic, bacterial
and archaeal genomes.
Can be searched using
accession numbers or
sought features |
|
libGenome |
A cross platform C++
development library to
manipulate DNA and
protein sequences. It
can read and write
sequence and annotation
data in several file
formats. |
|
GRIL |
GRIL automates the
process of identifying
large-scale genome
inversions and
rearrangements |
|
GRS |
A Graphic Tool for
Genome Retrieval and
Segment Analysis |
|
GenomePixelizer |
Genome Visualization
Tool: Detection of
duplicating events in
genomes, Displaying the
Genetic Maps,
Comparative genetics in
general. |
|
gff2ps |
Converting genomic
annotations in GFF
format to PostScript |
|
Acedb |
Acedb is a genome
database system
originally developed for
the C.elegans genome
project |
|
Clann |
Clann: Software for
investigating
phylogenomic information
using supertrees. This
implements several
methods of Supertree
analysis (which are used
as optimality criteria)
and allows exhaustive
and heuristic searches
of tree-space to find
the best supert |
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
gff2ps |
Converting genomic
annotations in GFF
format to PostScript |
|
UltraScan |
UltraScan is a
comprehensive GUI
editing and data
analysis package for
hydrodynamic data from
analytical
ultracentrifugation
experiments |
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|
PhyloGrapher |
PhyloGrapher is a
program designed to
visualize and study
evolutional relationship
between families of
homologous genes or
proteins. PhyloGrapher
is a drawing tool that
generates custom graphs
out of the given set of
genes based on distance
matrix file. |
|
Biogrep |
A grep that is
optimized for
biosequences. Biogrep is
designed to locate large
sets of patterns in
sequence databases in
parallel. |
|
Amplicon |
Program for
designing group-specific
PCR primer sets |
|
HMMER |
Profile hidden
Markov models for
biological sequence
analysis |
|
SAM equence Alignment
and Modeling Syste |
a collection of
flexible software tools
for creating, refining,
and using linear hidden
Markov models for
biological sequence
analysis |
|
VEIL |
A hidden Markov
model for finding genes
in vertebrate DNA? |
|
PhyloGrapher |
PhyloGrapher is a
program designed to
visualize and study
evolutional relationship
between families of
homologous genes or
proteins. PhyloGrapher
is a drawing tool that
generates custom graphs
out of the given set of
genes based on distance
matrix file. |
|
MOLPHY |
A Computer Program
Package for Molecular
Phylogenetics including
ProtML |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
Artemis |
a DNA sequence
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. |
|
BioJava |
The BioJava Project
is an open-source
project dedicated to
providing Java tools for
processing biological
data. |
|
MAExplorer |
The Microarray
Explorer (MAExplorer) is
a Java-based data-mining
facility for microarray
databases run as a
stand-alone program. It
includes graphics,
statistics, clustering,
reports, data filtering. |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
libGenome |
A cross platform C++
development library to
manipulate DNA and
protein sequences. It
can read and write
sequence and annotation
data in several file
formats. |
|
fastDNAml |
Estimates maximum
likelihood phylogenetic
trees from nucleotide
sequences |
|
MOLPHY |
A Computer Program
Package for Molecular
Phylogenetics including
ProtML |
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
TREE-PUZZLE: |
TREE-PUZZLE: Maximum
likelihood analysis for
nucleotide, amino acid,
and two-state data |
|
TREE-PUZZLE: |
TREE-PUZZLE: Maximum
likelihood analysis for
nucleotide, amino acid,
and two-state data |
|
MOLPHY |
A Computer Program
Package for Molecular
Phylogenetics including
ProtML |
|
fastDNAml |
Estimates maximum
likelihood phylogenetic
trees from nucleotide
sequences |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
BioMail |
automate searching
for recent scientific
papers in the PubMed
Medline database |
|
MELTING |
Accurate computation
of the enthalpy,
entropie and melting
temperature of a nucleic
acid duplex |
|
MAExplorer |
The Microarray
Explorer (MAExplorer) is
a Java-based data-mining
facility for microarray
databases run as a
stand-alone program. It
includes graphics,
statistics, clustering,
reports, data filtering. |
|
SEPON |
SEPON designs
gene-specific
oligonucleotides for
microarray experiments
and is able to use EST
input from organisms in
which the genome is not
annotated for genes.
SEPON implements a novel
algorithm for reducing
cross-hybridization by
utilizing thermodyna |
|
Teiresias-based Gene
expression analysis |
Discover patterns in
microarray data using
the Teiresias algorithm.
Allows discovery of
inversely regulated
genes. |
|
MAExplorer |
The Microarray
Explorer (MAExplorer) is
a Java-based data-mining
facility for microarray
databases run as a
stand-alone program. It
includes graphics,
statistics, clustering,
reports, data filtering. |
|
Teiresias-based Gene
expression analysis |
Discover patterns in
microarray data using
the Teiresias algorithm.
Allows discovery of
inversely regulated
genes. |
|
MAExplorer |
The Microarray
Explorer (MAExplorer) is
a Java-based data-mining
facility for microarray
databases run as a
stand-alone program. It
includes graphics,
statistics, clustering,
reports, data filtering. |
|
AMMP |
a modern
full-featured molecular
mechanics, dynamics and
modeling program. |
|
Kintecus |
Run chemical
kinetics/fitting of
catalyst reactor, and
enzyme reactions |
|
MMTK-2.2 |
molecular modeling
tool-kit 2.2 |
|
Oslet |
A molecular modeling
and simulation
environment in Java,
mainly for education. |
|
WHAT IF |
WHAT IF is a
versatile protein
structure analysis
program that can be used
for mutant prediction,
structure verification,
molecular graphics, etc |
|
Gromacs |
The World' s fastest
Molecular Dynamics - and
it' s gpl |
|
MMTK-2.2 |
molecular modeling
tool-kit 2.2 |
|
GDIS |
a GTK based program
for the display and
manipulation of isolated
molecules and periodic
systems |
|
PyMol |
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. |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
Oslet |
A molecular modeling
and simulation
environment in Java,
mainly for education. |
|
Spock |
a full-featured
molecular graphics
program |
|
AMMP |
a modern
full-featured molecular
mechanics, dynamics and
modeling program. |
|
Oslet |
A molecular modeling
and simulation
environment in Java,
mainly for education. |
|
WHAT IF |
WHAT IF is a
versatile protein
structure analysis
program that can be used
for mutant prediction,
structure verification,
molecular graphics, etc |
|
Babel |
a program designed
to interconvert a number
of file formats
currently used in
molecular modeling |
|
Garlic |
a free molecular
visualization program |
|
Oslet |
A molecular modeling
and simulation
environment in Java,
mainly for education. |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
Garlic |
a free molecular
visualization program |
|
rasmol |
RasMol is a free
program which displays
molecular structure.
|
|
VEGA |
VEGA was developed
to create a bridge
between most of the
molecular software
packages, like BioDock,
Quanta/CHARMm, Insight
II, MoPac, etc. In this
tool have been also
implemented some
features that are useful
to analyze, display and
manage the 3D struct |
|
VMD |
VMD is a molecular
visualization program
for displaying,
animating, and analyzing
large biomolecular
systems using 3-D
graphics and built-in
scripting |
|
Garlic |
a free molecular
visualization program |
|
XMolCalc |
a small utility that
allows you to calculate
a molecular weight |
|
UltraScan |
UltraScan is a
comprehensive GUI
editing and data
analysis package for
hydrodynamic data from
analytical
ultracentrifugation
experiments |
|
Biogrep |
A grep that is
optimized for
biosequences. Biogrep is
designed to locate large
sets of patterns in
sequence databases in
parallel. |
|
RNABOB |
RNABOB -- fast RNA
motif/pattern searcher |
|
mpiBLAST |
mpiBLAST is a
parallel implementation
of NCBI-BLAST that uses
database segmentation.
It achieves a
super-linear speedup in
some cases. |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
clustalw |
The famous ClustalW
multiple alignment
program |
|
clustalx |
Clustal X provides a
window-based user
interface to the
ClustalW multiple
alignment program |
|
DCSE |
DCSE (Dedicated
Comparative Sequence
Editor) is a multiple
alignment editor |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
Jalview |
Jalview - a java
multiple alignment
editor |
|
Mauve |
Mauve is a multiple
genome alignment and
visualization package
that considers
large-scale
rearrangements in
addition to nucleotide
substitution and indels. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
Musca |
Multiple sequence
alignment of aa or
nucleotide sequences /
uses pattern discovery |
|
MUSCLE |
Multiple sequence
alignment. More accurate
than T-Coffee, faster
than CLUSTALW. |
|
seaview |
SeaView is a
graphical multiple
sequence alignment
editor |
|
ShadyBox. |
ShadyBox. The FIRST
GUI based WYSIWYG
multiple sequence
alignment drawing
program for Major Unix
platforms |
|
DCSE |
DCSE (Dedicated
Comparative Sequence
Editor) is a multiple
alignment editor |
|
Jalview |
Jalview - a java
multiple alignment
editor |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
Mauve |
Mauve is a multiple
genome alignment and
visualization package
that considers
large-scale
rearrangements in
addition to nucleotide
substitution and indels. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
clustalw |
The famous ClustalW
multiple alignment
program |
|
clustalx |
Clustal X provides a
window-based user
interface to the
ClustalW multiple
alignment program |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
Musca |
Multiple sequence
alignment of aa or
nucleotide sequences /
uses pattern discovery |
|
MUSCLE |
Multiple sequence
alignment. More accurate
than T-Coffee, faster
than CLUSTALW. |
|
seaview |
SeaView is a
graphical multiple
sequence alignment
editor |
|
ShadyBox. |
ShadyBox. The FIRST
GUI based WYSIWYG
multiple sequence
alignment drawing
program for Major Unix
platforms |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
ShadyBox. |
ShadyBox. The FIRST
GUI based WYSIWYG
multiple sequence
alignment drawing
program for Major Unix
platforms |
|
Ensembl |
software system
which produces and
maintains automatic
annotation on
eukaryoticgenomes |
|
NAMD |
NAMD is a parallel,
object-oriented
molecular dynamics code
designed for
high-performance
simulation of large
biomolecular systems.
|
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
RNA GENiE |
A web based program
for the prediction of
rna genes in genomic DNA
sequences |
|
CNS |
The 'Crystallography
& NMR System' for
macromolecular structure
anaylsis |
|
MELTING |
Accurate computation
of the enthalpy,
entropie and melting
temperature of a nucleic
acid duplex |
|
Amplicon |
Program for
designing group-specific
PCR primer sets |
|
SEPON |
SEPON designs
gene-specific
oligonucleotides for
microarray experiments
and is able to use EST
input from organisms in
which the genome is not
annotated for genes.
SEPON implements a novel
algorithm for reducing
cross-hybridization by
utilizing thermodyna |
|
MPSRCH |
MPSRCH (tm) is a
suite of Smith-Waterman
sequence analysis
programs which run under
Linux and Tru64 on Intel
and Alpha. |
|
On-line Genome
Annotations |
Annotations for many
eukaryotic, bacterial
and archaeal genomes.
Can be searched using
accession numbers or
sought features |
|
mpiBLAST |
mpiBLAST is a
parallel implementation
of NCBI-BLAST that uses
database segmentation.
It achieves a
super-linear speedup in
some cases. |
|
Biogrep |
A grep that is
optimized for
biosequences. Biogrep is
designed to locate large
sets of patterns in
sequence databases in
parallel. |
|
Musca |
Multiple sequence
alignment of aa or
nucleotide sequences /
uses pattern discovery |
|
PatScan |
PatScan is a pattern
matcher which searches
protein or nucleotide
(DNA, RNA, tRNA etc.)
sequence archives for
instances of a pattern
which you input |
|
Pratt |
a pattern discovery
tool |
|
Musca |
Multiple sequence
alignment of aa or
nucleotide sequences /
uses pattern discovery |
|
PatScan |
PatScan is a pattern
matcher which searches
protein or nucleotide
(DNA, RNA, tRNA etc.)
sequence archives for
instances of a pattern
which you input |
|
Biogrep |
A grep that is
optimized for
biosequences. Biogrep is
designed to locate large
sets of patterns in
sequence databases in
parallel. |
|
Amplicon |
Program for
designing group-specific
PCR primer sets |
|
Garlic |
a free molecular
visualization program |
|
MMTK-2.2 |
molecular modeling
tool-kit 2.2 |
|
GEANFAMMER |
GEnome ANalysis and
Protein FAMily MakER |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
ATV |
a phylogenetic tree
display tool |
|
fastDNAml |
Estimates maximum
likelihood phylogenetic
trees from nucleotide
sequences |
|
njplot |
NJplot is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format |
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
Paup |
Software package for
inference of
evolutionary trees |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
PHYLIP |
PHYLIP is a free
package of programs for
inferring phylogenies. |
|
PhyloDraw |
PhyloDraw is a
drawing tool for
creating phylogenetic
trees. PhyloDraw
supports various kinds
of multialignment
programs (Dialign2,
Clustal-W, Phylip
format, and pairwise
distance matrix) and
visualizes various kinds
of tree diagrams, e.g.
rectangular cl |
|
phylowin |
Phylo_win is a
graphical colour
interface for molecular
phylogenetic inference.
|
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
unrooted |
Unrooted is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format in an
unrooted way, that is,
using a circular shape,
with labels aligned with
terminal branches.
|
|
ATV |
a phylogenetic tree
display tool |
|
fastDNAml |
Estimates maximum
likelihood phylogenetic
trees from nucleotide
sequences |
|
njplot |
NJplot is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format |
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
Paup |
Software package for
inference of
evolutionary trees |
|
PHYLIP |
PHYLIP is a free
package of programs for
inferring phylogenies. |
|
PhyloDraw |
PhyloDraw is a
drawing tool for
creating phylogenetic
trees. PhyloDraw
supports various kinds
of multialignment
programs (Dialign2,
Clustal-W, Phylip
format, and pairwise
distance matrix) and
visualizes various kinds
of tree diagrams, e.g.
rectangular cl |
|
phylowin |
Phylo_win is a
graphical colour
interface for molecular
phylogenetic inference.
|
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
unrooted |
Unrooted is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format in an
unrooted way, that is,
using a circular shape,
with labels aligned with
terminal branches.
|
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
ATV |
a phylogenetic tree
display tool |
|
fastDNAml |
Estimates maximum
likelihood phylogenetic
trees from nucleotide
sequences |
|
njplot |
NJplot is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format |
|
Paup |
Software package for
inference of
evolutionary trees |
|
PHYLIP |
PHYLIP is a free
package of programs for
inferring phylogenies. |
|
phylowin |
Phylo_win is a
graphical colour
interface for molecular
phylogenetic inference.
|
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
unrooted |
Unrooted is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format in an
unrooted way, that is,
using a circular shape,
with labels aligned with
terminal branches.
|
|
Clann |
Clann: Software for
investigating
phylogenomic information
using supertrees. This
implements several
methods of Supertree
analysis (which are used
as optimality criteria)
and allows exhaustive
and heuristic searches
of tree-space to find
the best supert |
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
Clann |
Clann: Software for
investigating
phylogenomic information
using supertrees. This
implements several
methods of Supertree
analysis (which are used
as optimality criteria)
and allows exhaustive
and heuristic searches
of tree-space to find
the best supert |
|
Clann |
Clann: Software for
investigating
phylogenomic information
using supertrees. This
implements several
methods of Supertree
analysis (which are used
as optimality criteria)
and allows exhaustive
and heuristic searches
of tree-space to find
the best supert |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
MOLPHY |
A Computer Program
Package for Molecular
Phylogenetics including
ProtML |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
PhyloGrapher |
PhyloGrapher is a
program designed to
visualize and study
evolutional relationship
between families of
homologous genes or
proteins. PhyloGrapher
is a drawing tool that
generates custom graphs
out of the given set of
genes based on distance
matrix file. |
|
gff2ps |
Converting genomic
annotations in GFF
format to PostScript |
|
Deep View
Swiss-PdbViewer |
Swiss-PdbViewer is
an application that
provides a user friendly
interface allowing to
analyse several proteins
at the same time |
|
caRNAc |
RNA secondary
structure inference for
set of homologous
sequences |
|
ConsInspector |
A tool for the
prediction of protein
binding sites in nucleic
acids |
|
geneid |
Gene prediction
tool, it can also
introduce homology and
annotation evidences and
produce a reannotation
of a genomic sequence. A
pthreads parallel
version also available. |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
Amplicon |
Program for
designing group-specific
PCR primer sets |
|
primer |
a program for
picking primers for PCR
reaction |
|
primer |
a program for
picking primers for PCR
reaction |
|
DIALIGN |
DIALIGN is an
alignment program that
relies on comparison of
whole segments of the
sequences instead of
comparison of single
residue |
|
Garlic |
a free molecular
visualization program |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
ShadyBox. |
ShadyBox. The FIRST
GUI based WYSIWYG
multiple sequence
alignment drawing
program for Major Unix
platforms |
|
ProSA |
ProSA is a useful
web application for
finding known protein
domains in
nucleotide/protein
sequences via PROSITE
database searching |
|
ConsInspector |
A tool for the
prediction of protein
binding sites in nucleic
acids |
|
ZDOCK |
Protein-protein
complex structure
prediction software |
|
DomainFinder |
DomainFinder 1.0
DomainFinder is an
interactive program for
the determination and
characterization of
dynamical domains in
proteins |
|
ProSA |
ProSA is a useful
web application for
finding known protein
domains in
nucleotide/protein
sequences via PROSITE
database searching |
|
GEANFAMMER |
GEnome ANalysis and
Protein FAMily MakER |
|
ZDOCK |
Protein-protein
complex structure
prediction software |
|
BRAGI |
BRAGI is a
interactive protein
modelling and display
program. It was
developed for the
special purpose to
modell unknown proteins
from the structure of a
known one |
|
Abacus |
ABaCUS is a
no-frills program
developed to investigate
the significance of the
putative correspondence
between exons and units
of protein structure. |
|
Garlic |
a free molecular
visualization program |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
MODELLER |
a program for
homology protein
structure modelling by
satisfaction of spatial
restraints. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
MODELLER |
a program for
homology protein
structure modelling by
satisfaction of spatial
restraints. |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
BioMail |
automate searching
for recent scientific
papers in the PubMed
Medline database |
|
Biopython |
The Biopython
Project is an
international
association of
developers of freely
available Python tools
for computational
molecular biology. |
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
PyMol |
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. |
|
geneid |
Gene prediction
tool, it can also
introduce homology and
annotation evidences and
produce a reannotation
of a genomic sequence. A
pthreads parallel
version also available. |
|
Biogrep |
A grep that is
optimized for
biosequences. Biogrep is
designed to locate large
sets of patterns in
sequence databases in
parallel. |
|
Biogrep |
A grep that is
optimized for
biosequences. Biogrep is
designed to locate large
sets of patterns in
sequence databases in
parallel. |
|
Toucan |
A Java tool for
regulatory sequence
analysis: detecting
over-represented motifs
and modules in sets of
co-regulated genes. |
|
GDIS |
a GTK based program
for the display and
manipulation of isolated
molecules and periodic
systems |
|
caRNAc |
RNA secondary
structure inference for
set of homologous
sequences |
|
caRNAsta |
Comparative Analysis
of RNA structures by
Tree Alignment |
|
cove |
COVE is an
implementation of
stochastic context free
grammar methods for RNA
sequence/structure
analysis. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
NCRNASCAN |
a structural RNA
genefinder |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
PKNOTS |
RNA pseudoknot
prediction |
|
RNA GENiE |
A web based program
for the prediction of
rna genes in genomic DNA
sequences |
|
RNABOB |
RNABOB -- fast RNA
motif/pattern searcher |
|
RnaViz |
a user-friendly,
portable, GUI program
for producing
publication-quality
secondary structure
drawings of RNA
molecules. Drawings |
|
tRNAscan-SE |
tRNA detection in
genome sequences,
detects ~99% of
eukaryotic nuclear or
prokaryotic tRNA genes,
with a false positive
rate of less than one
per 15 gigabases, and
with a search speed of
about 30 kb/second. |
|
Vienna RNA Package |
RNA Secondary
Structure Prediction and
Comparison |
|
RNABOB |
RNABOB -- fast RNA
motif/pattern searcher |
|
PKNOTS |
RNA pseudoknot
prediction |
|
caRNAsta |
Comparative Analysis
of RNA structures by
Tree Alignment |
|
cove |
COVE is an
implementation of
stochastic context free
grammar methods for RNA
sequence/structure
analysis. |
|
caRNAsta |
Comparative Analysis
of RNA structures by
Tree Alignment |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
phred |
Phred reads DNA
sequencer trace data,
calls bases, assigns
quality values to the
bases, and writes the
base calls and quality
values to output files. |
|
caRNAsta |
Comparative Analysis
of RNA structures by
Tree Alignment |
|
cove |
COVE is an
implementation of
stochastic context free
grammar methods for RNA
sequence/structure
analysis. |
|
RnaViz |
a user-friendly,
portable, GUI program
for producing
publication-quality
secondary structure
drawings of RNA
molecules. Drawings |
|
SEPON |
SEPON designs
gene-specific
oligonucleotides for
microarray experiments
and is able to use EST
input from organisms in
which the genome is not
annotated for genes.
SEPON implements a novel
algorithm for reducing
cross-hybridization by
utilizing thermodyna |
|
ARB |
Microbiologist's
sequence database tool |
|
Artemis |
a DNA sequence
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. |
|
autoseq |
a small package of
base calling software
for ABI automated DNA
sequencers |
|
Biogrep |
A grep that is
optimized for
biosequences. Biogrep is
designed to locate large
sets of patterns in
sequence databases in
parallel. |
|
BioJava |
The BioJava Project
is an open-source
project dedicated to
providing Java tools for
processing biological
data. |
|
Biopython |
The Biopython
Project is an
international
association of
developers of freely
available Python tools
for computational
molecular biology. |
|
BioWish |
Biowish is a
C-extension for the
Tcl/Tk scripting
language |
|
Blast |
BLAST (Basic Local
Alignment Search Tool)
is a set of similarity
search programs designed
to explore all of the
available sequence
databases |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
clustalw |
The famous ClustalW
multiple alignment
program |
|
clustalx |
Clustal X provides a
window-based user
interface to the
ClustalW multiple
alignment program |
|
consed |
A Unix-based
Graphical Editor and
Automated Finishing
Program for Phrap
Sequence Assemblies |
|
DBWatcher |
DBWatcher is a
program handling
periodic BLAST searches
to find similarities to
your own sequences. |
|
DNA-GUI |
DNA Graphical User
Interface |
|
EMBOSS |
EMBOSS is a package
of high-quality FREE
Open Source software for
sequence analysis. |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
gBioSeq |
Biological sequence
(ADN, protein) editor
for GTK/Linux |
|
Genpak |
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 |
|
JAligner |
JAligner is a Java
implementation of
biological sequence
alignment algorithms. |
|
libGenome |
A cross platform C++
development library to
manipulate DNA and
protein sequences. It
can read and write
sequence and annotation
data in several file
formats. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
MPSRCH |
MPSRCH (tm) is a
suite of Smith-Waterman
sequence analysis
programs which run under
Linux and Tru64 on Intel
and Alpha. |
|
Musca |
Multiple sequence
alignment of aa or
nucleotide sequences /
uses pattern discovery |
|
MUSCLE |
Multiple sequence
alignment. More accurate
than T-Coffee, faster
than CLUSTALW. |
|
NCRNASCAN |
a structural RNA
genefinder |
|
PatScan |
PatScan is a pattern
matcher which searches
protein or nucleotide
(DNA, RNA, tRNA etc.)
sequence archives for
instances of a pattern
which you input |
|
PhyloDraw |
PhyloDraw is a
drawing tool for
creating phylogenetic
trees. PhyloDraw
supports various kinds
of multialignment
programs (Dialign2,
Clustal-W, Phylip
format, and pairwise
distance matrix) and
visualizes various kinds
of tree diagrams, e.g.
rectangular cl |
|
PKNOTS |
RNA pseudoknot
prediction |
|
Pratt |
a pattern discovery
tool |
|
readseq |
Reads and writes
nucleic/protein
sequences in various
format |
|
SAM equence Alignment
and Modeling Syste |
a collection of
flexible software tools
for creating, refining,
and using linear hidden
Markov models for
biological sequence
analysis |
|
SEALS |
SEALS (A System for
Easy Analysis of Lots of
Sequences) is a software
package expressly
designed for large-scale
research projects in
bioinformatics. |
|
seaview |
SeaView is a
graphical multiple
sequence alignment
editor |
|
SeqPup |
SeqPup biological
sequence editor and
analysis program |
|
ShadyBox. |
ShadyBox. The FIRST
GUI based WYSIWYG
multiple sequence
alignment drawing
program for Major Unix
platforms |
|
sp2fasta |
produce a file in
FASTA format from one in
SWISSPROTor EMBL flat
file format |
|
Toucan |
A Java tool for
regulatory sequence
analysis: detecting
over-represented motifs
and modules in sets of
co-regulated genes. |
|
tRNAscan-SE |
tRNA detection in
genome sequences,
detects ~99% of
eukaryotic nuclear or
prokaryotic tRNA genes,
with a false positive
rate of less than one
per 15 gigabases, and
with a search speed of
about 30 kb/second. |
|
WU-Blast |
Washington U. Blast |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
clustalw |
The famous ClustalW
multiple alignment
program |
|
clustalx |
Clustal X provides a
window-based user
interface to the
ClustalW multiple
alignment program |
|
JAligner |
JAligner is a Java
implementation of
biological sequence
alignment algorithms. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
Musca |
Multiple sequence
alignment of aa or
nucleotide sequences /
uses pattern discovery |
|
MUSCLE |
Multiple sequence
alignment. More accurate
than T-Coffee, faster
than CLUSTALW. |
|
PhyloDraw |
PhyloDraw is a
drawing tool for
creating phylogenetic
trees. PhyloDraw
supports various kinds
of multialignment
programs (Dialign2,
Clustal-W, Phylip
format, and pairwise
distance matrix) and
visualizes various kinds
of tree diagrams, e.g.
rectangular cl |
|
SAM equence Alignment
and Modeling Syste |
a collection of
flexible software tools
for creating, refining,
and using linear hidden
Markov models for
biological sequence
analysis |
|
seaview |
SeaView is a
graphical multiple
sequence alignment
editor |
|
ShadyBox. |
ShadyBox. The FIRST
GUI based WYSIWYG
multiple sequence
alignment drawing
program for Major Unix
platforms |
|
ARB |
Microbiologist's
sequence database tool |
|
BioJava |
The BioJava Project
is an open-source
project dedicated to
providing Java tools for
processing biological
data. |
|
Biopython |
The Biopython
Project is an
international
association of
developers of freely
available Python tools
for computational
molecular biology. |
|
BioWish |
Biowish is a
C-extension for the
Tcl/Tk scripting
language |
|
Blast |
BLAST (Basic Local
Alignment Search Tool)
is a set of similarity
search programs designed
to explore all of the
available sequence
databases |
|
clustalw |
The famous ClustalW
multiple alignment
program |
|
clustalx |
Clustal X provides a
window-based user
interface to the
ClustalW multiple
alignment program |
|
DNA-GUI |
DNA Graphical User
Interface |
|
EMBOSS |
EMBOSS is a package
of high-quality FREE
Open Source software for
sequence analysis. |
|
MPSRCH |
MPSRCH (tm) is a
suite of Smith-Waterman
sequence analysis
programs which run under
Linux and Tru64 on Intel
and Alpha. |
|
NCRNASCAN |
a structural RNA
genefinder |
|
PatScan |
PatScan is a pattern
matcher which searches
protein or nucleotide
(DNA, RNA, tRNA etc.)
sequence archives for
instances of a pattern
which you input |
|
PKNOTS |
RNA pseudoknot
prediction |
|
Pratt |
a pattern discovery
tool |
|
readseq |
Reads and writes
nucleic/protein
sequences in various
format |
|
SEALS |
SEALS (A System for
Easy Analysis of Lots of
Sequences) is a software
package expressly
designed for large-scale
research projects in
bioinformatics. |
|
sp2fasta |
produce a file in
FASTA format from one in
SWISSPROTor EMBL flat
file format |
|
Toucan |
A Java tool for
regulatory sequence
analysis: detecting
over-represented motifs
and modules in sets of
co-regulated genes. |
|
tRNAscan-SE |
tRNA detection in
genome sequences,
detects ~99% of
eukaryotic nuclear or
prokaryotic tRNA genes,
with a false positive
rate of less than one
per 15 gigabases, and
with a search speed of
about 30 kb/second. |
|
WU-Blast |
Washington U. Blast |
|
DBWatcher |
DBWatcher is a
program handling
periodic BLAST searches
to find similarities to
your own sequences. |
|
readseq |
Reads and writes
nucleic/protein
sequences in various
format |
|
sp2fasta |
produce a file in
FASTA format from one in
SWISSPROTor EMBL flat
file format |
|
ARB |
Microbiologist's
sequence database tool |
|
gBioSeq |
Biological sequence
(ADN, protein) editor
for GTK/Linux |
|
SeqPup |
SeqPup biological
sequence editor and
analysis program |
|
consed |
A Unix-based
Graphical Editor and
Automated Finishing
Program for Phrap
Sequence Assemblies |
|
Pratt |
a pattern discovery
tool |
|
Blast |
BLAST (Basic Local
Alignment Search Tool)
is a set of similarity
search programs designed
to explore all of the
available sequence
databases |
|
Genpak |
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 |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
autoseq |
a small package of
base calling software
for ABI automated DNA
sequencers |
|
consed |
A Unix-based
Graphical Editor and
Automated Finishing
Program for Phrap
Sequence Assemblies |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
phred |
Phred reads DNA
sequencer trace data,
calls bases, assigns
quality values to the
bases, and writes the
base calls and quality
values to output files. |
|
JAligner |
JAligner is a Java
implementation of
biological sequence
alignment algorithms. |
|
MPSRCH |
MPSRCH (tm) is a
suite of Smith-Waterman
sequence analysis
programs which run under
Linux and Tru64 on Intel
and Alpha. |
|
Steric |
A Program to
Calculate the Steric
Size of Molecules about
a Point in terms of
their Cone Angles and
Solid Angles, as well as
their total Volumes and
Projected Areas |
|
Staden Package |
This is a free to
academics (charge for
commercial users)
package including
sequence assemble, trace
viewing/editing and
sequence analysis tools.
It also includes a GUI
to the free EMBOSS
suite. |
|
Oslet |
A molecular modeling
and simulation
environment in Java,
mainly for education. |
|
Steric |
A Program to
Calculate the Steric
Size of Molecules about
a Point in terms of
their Cone Angles and
Solid Angles, as well as
their total Volumes and
Projected Areas |
|
Deep View
Swiss-PdbViewer |
Swiss-PdbViewer is
an application that
provides a user friendly
interface allowing to
analyse several proteins
at the same time |
|
DINO |
a realtime 3D
visualization program
for structural biology
data. |
|
Abacus |
ABaCUS is a
no-frills program
developed to investigate
the significance of the
putative correspondence
between exons and units
of protein structure. |
|
caRNAc |
RNA secondary
structure inference for
set of homologous
sequences |
|
caRNAsta |
Comparative Analysis
of RNA structures by
Tree Alignment |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
CNS |
The 'Crystallography
& NMR System' for
macromolecular structure
anaylsis |
|
cove |
COVE is an
implementation of
stochastic context free
grammar methods for RNA
sequence/structure
analysis. |
|
Garlic |
a free molecular
visualization program |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
MODELLER |
a program for
homology protein
structure modelling by
satisfaction of spatial
restraints. |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
MOPAC7 |
a general-purpose
semi-empirical molecular
orbital package for the
study of chemical
structures and
reactions. |
|
PyMol |
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. |
|
RNA GENiE |
A web based program
for the prediction of
rna genes in genomic DNA
sequences |
|
RnaViz |
a user-friendly,
portable, GUI program
for producing
publication-quality
secondary structure
drawings of RNA
molecules. Drawings |
|
Chimera |
Excellent molecular
graphics package with
support for a wide range
of operations, i
ncluding flexible
molecular graphics, high
resolution images for
publication, user-driven
analysis, multiple
sequence alignment
analysis, multiple model
analysis, dockin |
|
CNS |
The 'Crystallography
& NMR System' for
macromolecular structure
anaylsis |
|
caRNAc |
RNA secondary
structure inference for
set of homologous
sequences |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
sp2fasta |
produce a file in
FASTA format from one in
SWISSPROTor EMBL flat
file format |
|
BioWish |
Biowish is a
C-extension for the
Tcl/Tk scripting
language |
|
caRNAc |
RNA secondary
structure inference for
set of homologous
sequences |
|
MELTING |
Accurate computation
of the enthalpy,
entropie and melting
temperature of a nucleic
acid duplex |
|
LIBELLULA |
LIBELLULA is a
neural network based web
server to evaluate fold
recognition results |
|
io_lib |
An open source C
library of sequence
trace files supporting
ABI, ALF, SCF, CTF and
ZTR file formats. |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
phred |
Phred reads DNA
sequencer trace data,
calls bases, assigns
quality values to the
bases, and writes the
base calls and quality
values to output files. |
|
Staden Package |
This is a free to
academics (charge for
commercial users)
package including
sequence assemble, trace
viewing/editing and
sequence analysis tools.
It also includes a GUI
to the free EMBOSS
suite. |
|
UltraScan |
UltraScan is a
comprehensive GUI
editing and data
analysis package for
hydrodynamic data from
analytical
ultracentrifugation
experiments |
|
io_lib |
An open source C
library of sequence
trace files supporting
ABI, ALF, SCF, CTF and
ZTR file formats. |
|
phrap |
a program for
assembling shotgun DNA
sequence data |
|
phred |
Phred reads DNA
sequencer trace data,
calls bases, assigns
quality values to the
bases, and writes the
base calls and quality
values to output files. |
|
VEGA |
VEGA was developed
to create a bridge
between most of the
molecular software
packages, like BioDock,
Quanta/CHARMm, Insight
II, MoPac, etc. In this
tool have been also
implemented some
features that are useful
to analyze, display and
manage the 3D struct |
|
GenomeInspector |
Software for the
analysis of spatial
correlations of elements
on DNA sequences |
|
Toucan |
A Java tool for
regulatory sequence
analysis: detecting
over-represented motifs
and modules in sets of
co-regulated genes. |
|
ATV |
a phylogenetic tree
display tool |
|
Clann |
Clann: Software for
investigating
phylogenomic information
using supertrees. This
implements several
methods of Supertree
analysis (which are used
as optimality criteria)
and allows exhaustive
and heuristic searches
of tree-space to find
the best supert |
|
fastDNAml |
Estimates maximum
likelihood phylogenetic
trees from nucleotide
sequences |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
njplot |
NJplot is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format |
|
PAML |
Phylogenetic
Analysis by Maximum
Likelihood |
|
Paup |
Software package for
inference of
evolutionary trees |
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
PHYLIP |
PHYLIP is a free
package of programs for
inferring phylogenies. |
|
PhyloDraw |
PhyloDraw is a
drawing tool for
creating phylogenetic
trees. PhyloDraw
supports various kinds
of multialignment
programs (Dialign2,
Clustal-W, Phylip
format, and pairwise
distance matrix) and
visualizes various kinds
of tree diagrams, e.g.
rectangular cl |
|
phylowin |
Phylo_win is a
graphical colour
interface for molecular
phylogenetic inference.
|
|
PyPhy |
PyPhy is a set of
python scripts and
modules for automatic,
large-scale
reconstructions of
phylogenetic
relationships of
complete microbial
genomes. |
|
unrooted |
Unrooted is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format in an
unrooted way, that is,
using a circular shape,
with labels aligned with
terminal branches.
|
|
PHASE |
PHASE performs
molecular phylogenetic
inference using maximum
likelihood and Bayesian
(MCMC) techniques.
Specific RNA
substitution models are
implemented to account
for the correlated
mutations of paired
bases in RNA helices. |
|
ATV |
a phylogenetic tree
display tool |
|
njplot |
NJplot is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format |
|
phylowin |
Phylo_win is a
graphical colour
interface for molecular
phylogenetic inference.
|
|
unrooted |
Unrooted is a tree
drawing program able to
draw any binary tree
expressed in the
standard phylogenetic
tree format in an
unrooted way, that is,
using a circular shape,
with labels aligned with
terminal branches.
|
|
tRNAscan-SE |
tRNA detection in
genome sequences,
detects ~99% of
eukaryotic nuclear or
prokaryotic tRNA genes,
with a false positive
rate of less than one
per 15 gigabases, and
with a search speed of
about 30 kb/second. |
|
Friend |
Friend, an
Integrated Front-end
Application for
Bioinformatics |
|
Garlic |
a free molecular
visualization program |
|
GeneView II |
Interactive GenBank
Entry Visualization |
|
gff2ps |
Converting genomic
annotations in GFF
format to PostScript |
|
ModView |
ModView is a program
to visualize and analyze
multiple biomolecule
structures and/or
sequence alignments. |
|
PyMol |
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. |
|
rasmol |
RasMol is a free
program which displays
molecular structure.
|
|
VEGA |
VEGA was developed
to create a bridge
between most of the
molecular software
packages, like BioDock,
Quanta/CHARMm, Insight
II, MoPac, etc. In this
tool have been also
implemented some
features that are useful
to analyze, display and
manage the 3D struct |
|
VMD |
VMD is a molecular
visualization program
for displaying,
animating, and analyzing
large biomolecular
systems using 3-D
graphics and built-in
scripting |
|
NAMD |
NAMD is a parallel,
object-oriented
molecular dynamics code
designed for
high-performance
simulation of large
biomolecular systems.
|
|
Sight |
Allows programming
free assembling of web
resoureces, local
executables and ssh
services into arbitrary
workflow. |
|
Sight |
Allows programming
free assembling of web
resoureces, local
executables and ssh
services into arbitrary
workflow. |
|
OmniGene |
Standardizing
Biological Data
Interchange Through Web
Services Technology |
|
|
|
