| Description: |
Automatic Image processing for Microarrays |
| Author(s): |
Mathias Katzer |
| Platform: |
linux.i586.glibc61, linux.i586.glibc62 |
|
| Description: |
Automatic Image processing for Microarrays |
| Author(s): |
Mathias Katzer |
| Platform: |
linux.i586 |
|
| Description: |
Bpr is an implementation of the 'bucket-pointer
refinement' construction algorithm for suffix
arrays |
| Author(s): |
Klaus-Bernd Schürmann, Jens Stoye |
| Platform: |
src, src, none, none |
|
| Description: |
DCA is a very fast sequence alignment algorithm
producing high quality alignments (close to the optimal
alignment under the sum-of-pairs score). |
| Author(s): |
Jens Stoye |
| Platform: |
src |
|
| Description: |
DIALIGN is a novel alignment program based on
segment-to-segment comparison.It is especially suited
to detect local similarities among distantly related
sequences. |
| Author(s): |
Burkhard Morgenstern, Said Abdeddaim |
| Platform: |
src, solaris.sparc.v8, solaris.sparc.static,
solaris.x86.v10, linux.i586, linux.i586.static,
dec.alpha, mac, osx, sgi |
|
| Description: |
Gene cluster detection in prokaryotic genomes |
| Author(s): |
Katharina Jahn and Leon Kuchenbecker |
| Platform: |
java.1.4 |
|
| Description: |
Gene cluster detection in prokaryotic genomes |
| Author(s): |
Katharina Jahn and Leon Kuchenbecker |
| Platform: |
java.1.4 |
|
| Description: |
Gene cluster detection in prokaryotic genomes |
| Author(s): |
Katharina Jahn and Leon Kuchenbecker |
| Platform: |
java.1.4, java.1.5, java.1.6, src, java,
java.1.6 |
|
| Description: |
Gene cluster detection in prokaryotic genomes |
| Author(s): |
Katharina Jahn and Leon Kuchenbecker |
| Platform: |
java.1.6 |
|
| Description: |
A utility for fast exact matching under RNA base
pairing rules |
| Author(s): |
Wolfgang Gerlach |
| Platform: |
src |
|
| Description: |
A utility for fast exact matching under RNA base
pairing rules |
| Author(s): |
Wolfgang Gerlach |
| Platform: |
src |
|
| Description: |
A utility for fast exact matching under RNA base
pairing rules |
| Author(s): |
Wolfgang Gerlach |
| Platform: |
src |
|
| Description: |
Intrinsic and Extrinsic Prediction of mature
miRNA. |
| Author(s): |
Sylvia Tippmann, Jan Krüger |
| Platform: |
java |
|
| Description: |
Intrinsic and Extrinsic Prediction of mature
miRNA. |
| Author(s): |
Sylvia Tippmann, Jan Krüger |
| Platform: |
java |
|
| Description: |
Jumping Alignments Jali is an alignment method for
comparing a protein sequence to a protein family,
represented by a multiple alignment. It can also be
used for sensitive protein database searches. The
algorithm is a generalization of the Smith-Watherman
algorithm. |
| Author(s): |
Jens Stoye, Constantin Bannert |
| Platform: |
solaris.sparc.v2.10, solaris.x86.v2.10,
linux-ubuntu.x86.9.10, linux-ubuntu.x86.10.4,
osx.x86.10.6, src |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java, src |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java, src |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java, src |
|
| Description: |
jPREdictor is a tool for the prediction of
cis-regulatory elements, e.g. PRE/TREs in Drosophila
melanogaster. |
| Author(s): |
Thomas Fiedler |
| Platform: |
java, src |
|
| Description: |
The Full-text Index Data structure library, libfid
for short, is a portable software library for accessing
indexed data through a simple C interface. It
implements, among others, functions for reading indexed
data from files, and performing common operations such
as fast string matching on these. Easy alphabet
handling for mapping between printable and binary
alphabets is integrated from the ground up. Currently,
the enhanced suffix array is the only full-text index
data structure supported. A very simplistic program for
constructing enhanced suffix arrays is included. The
library is freely available as source code under the
terms of the GNU Lesser General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src, data |
|
| Description: |
The Full-text Index Data structure library, libfid
for short, is a portable software library for accessing
indexed data through a simple C interface. It
implements, among others, functions for reading indexed
data from files, and performing common operations such
as fast string matching on these. Easy alphabet
handling for mapping between printable and binary
alphabets is integrated from the ground up. Currently,
the enhanced suffix array is the only full-text index
data structure supported. A very simplistic program for
constructing enhanced suffix arrays is included. The
library is freely available as source code under the
terms of the GNU Lesser General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src, data |
|
| Description: |
The Full-text Index Data structure library, libfid
for short, is a portable software library for accessing
indexed data through a simple C interface. It
implements, among others, functions for reading indexed
data from files, and performing common operations such
as fast string matching on these. Easy alphabet
handling for mapping between printable and binary
alphabets is integrated from the ground up. Currently,
the enhanced suffix array is the only full-text index
data structure supported. A very simplistic program for
constructing enhanced suffix arrays is included. The
library is freely available as source code under the
terms of the GNU Lesser General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src, data, data |
|
| Description: |
The Full-text Index Data structure library, libfid
for short, is a portable software library for accessing
indexed data through a simple C interface. It
implements, among others, functions for reading indexed
data from files, and performing common operations such
as fast string matching on these. Easy alphabet
handling for mapping between printable and binary
alphabets is integrated from the ground up. Currently,
the enhanced suffix array is the only full-text index
data structure supported. A very simplistic program for
constructing enhanced suffix arrays is included. The
library is freely available as source code under the
terms of the GNU Lesser General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src, data, data |
|
| Description: |
The Full-text Index Data structure library, libfid
for short, is a portable software library for accessing
indexed data through a simple C interface. It
implements, among others, functions for reading indexed
data from files, and performing common operations such
as fast string matching on these. Easy alphabet
handling for mapping between printable and binary
alphabets is integrated from the ground up. Currently,
the enhanced suffix array is the only full-text index
data structure supported. A very simplistic program for
constructing enhanced suffix arrays is included. The
library is freely available as source code under the
terms of the GNU Lesser General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src, data, data |
|
| Description: |
The Full-text Index Data structure library, libfid
for short, is a portable software library for accessing
indexed data through a simple C interface. It
implements, among others, functions for reading indexed
data from files, and performing common operations such
as fast string matching on these. Easy alphabet
handling for mapping between printable and binary
alphabets is integrated from the ground up. Currently,
the enhanced suffix array is the only full-text index
data structure supported. A very simplistic program for
constructing enhanced suffix arrays is included. The
library is freely available as source code under the
terms of the GNU Lesser General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src, data, data |
|
| Description: |
The Full-text Index Data structure library, libfid
for short, is a portable software library for accessing
indexed data through a simple C interface. It
implements, among others, functions for reading indexed
data from files, and performing common operations such
as fast string matching on these. Easy alphabet
handling for mapping between printable and binary
alphabets is integrated from the ground up. Currently,
the enhanced suffix array is the only full-text index
data structure supported. A very simplistic program for
constructing enhanced suffix arrays is included. The
library is freely available as source code under the
terms of the GNU Lesser General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src, data, data |
|
| Description: |
The Full-text Index Data structure library, libfid
for short, is a portable software library for accessing
indexed data through a simple C interface. It
implements, among others, functions for reading indexed
data from files, and performing common operations such
as fast string matching on these. Easy alphabet
handling for mapping between printable and binary
alphabets is integrated from the ground up. Currently,
the enhanced suffix array is the only full-text index
data structure supported. A very simplistic program for
constructing enhanced suffix arrays is included. The
library is freely available as source code under the
terms of the GNU Lesser General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src, data, data |
|
| Description: |
MGA efficiently computes multiple genome alignments
of large, closely related DNA sequences. |
| Author(s): |
Michael Hoehl, Stefan Kurtz, Enno Ohlebusch |
| Platform: |
solaris.sparc, linux.i586, dec.alpha |
|
| Description: |
mkESA is an open source program for constructing
enhanced suffix arrays (ESAs) from biological sequence
data. The program is based on our implementation of
Manzini's lightweight Deep-Shallow algorithm, which can
also utilize multiple CPUs/cores for some extra
speed-up. The generated output is compatible to the
output of mkvtree from the Vmatch package written by
Stefan Kurtz. mkESA is freely available as source code
under the terms of the GNU General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src |
|
| Description: |
mkESA is an open source program for constructing
enhanced suffix arrays (ESAs) from biological sequence
data. The program is based on our implementation of
Manzini's lightweight Deep-Shallow algorithm, which can
also utilize multiple CPUs/cores for some extra
speed-up. The generated output is compatible to the
output of mkvtree from the Vmatch package written by
Stefan Kurtz. mkESA is freely available as source code
under the terms of the GNU General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src |
|
| Description: |
mkESA is an open source program for constructing
enhanced suffix arrays (ESAs) from biological sequence
data. The program is based on our implementation of
Manzini's lightweight Deep-Shallow algorithm, which can
also utilize multiple CPUs/cores for some extra
speed-up. The generated output is compatible to the
output of mkvtree from the Vmatch package written by
Stefan Kurtz. mkESA is freely available as source code
under the terms of the GNU General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src |
|
| Description: |
mkESA is an open source program for constructing
enhanced suffix arrays (ESAs) from biological sequence
data. The program is based on our implementation of
Manzini's lightweight Deep-Shallow algorithm, which can
also utilize multiple CPUs/cores for some extra
speed-up. The generated output is compatible to the
output of mkvtree from the Vmatch package written by
Stefan Kurtz. mkESA is freely available as source code
under the terms of the GNU General Public License |
| Author(s): |
Robert Homann |
| Platform: |
src |
|
| Description: |
Optimal Multiple Sequence Alignment |
| Author(s): |
Thorsten Will, Knut Reinert, Jens Stoye |
| Platform: |
src |
|
| Description: |
Optimal Multiple Sequence Alignment |
| Author(s): |
Thorsten Will, Knut Reinert, Jens Stoye |
| Platform: |
solaris.sparc |
|
| Description: |
Simple retrieval of sequences |
| Author(s): |
Henning Mersch, Georg Fuellen |
| Platform: |
src |
|
| Description: |
Automatic evaluation of database search
methods. |
| Author(s): |
Marc Rehmsmeier |
| Platform: |
src |
|
| Description: |
pknotsRG is a tool for folding RNA secondary
structures, including the class of simple recursive
pseudoknots. |
| Author(s): |
Jens Reeder, Robert Giegerich |
| Platform: |
src |
|
| Description: |
pknotsRG is a tool for folding RNA secondary
structures, including the class of simple recursive
pseudoknots. |
| Author(s): |
Jens Reeder, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32 |
|
| Description: |
pknotsRG is a tool for folding RNA secondary
structures, including the class of simple recursive
pseudoknots. |
| Author(s): |
Jens Reeder, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32 |
|
| Description: |
pknotsRG is a tool for folding RNA secondary
structures, including the class of simple recursive
pseudoknots. |
| Author(s): |
Jens Reeder, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32, osx |
|
| Description: |
planACstar is an implementation of plan AC* that
improves structural RNA alignments by structure
comparison |
| Author(s): |
Andreas Bremges |
| Platform: |
src |
| require: |
BioPerl |
|
| Description: |
planACstar is an implementation of plan AC* that
improves structural RNA alignments by structure
comparison |
| Author(s): |
Andreas Bremges |
| Platform: |
src, src |
| require: |
BioPerl |
|
| Description: |
Fast and Sensitive Matching of Position Specific
Scoring Matrices Using Enhanced Suffix Arrays |
| Author(s): |
Michael Beckstette, Dirk Strothmann, Robert Homann,
Robert Giegerich, Stefan Kurtz |
| Platform: |
solaris.x86.v10, solaris.sparc.v8, linux.i586 |
|
| Description: |
Fast and Sensitive Matching of Position Specific
Scoring Matrices Using Enhanced Suffix Arrays |
| Author(s): |
Michael Beckstette, Dirk Strothmann, Robert Homann,
Robert Giegerich, Stefan Kurtz |
| Platform: |
solaris.x86.v10, solaris.sparc.v8, linux.i586,
linux.i686 |
|
| Description: |
Fast and Sensitive Matching of Position Specific
Scoring Matrices Using Enhanced Suffix Arrays |
| Author(s): |
Michael Beckstette, Dirk Strothmann, Robert Homann,
Robert Giegerich, Stefan Kurtz |
| Platform: |
solaris.x86.v10, solaris.sparc.v8, linux.i586,
linux.i686 |
|
| Description: |
Fast and Sensitive Matching of Position Specific
Scoring Matrices Using Enhanced Suffix Arrays |
| Author(s): |
Michael Beckstette, Dirk Strothmann, Robert Homann,
Robert Giegerich, Stefan Kurtz |
| Platform: |
linux.amd64, linux.x86, solaris.amd64.v10,
solaris.x86.v10, solaris.sparc.v8,
solaris.sparc.v8 |
|
| Description: |
Significant speedup of database searches with HMMs
by search space reduction with PSSM family models |
| Author(s): |
Michael Beckstette, Robert Homann, Robert
Giegerich, Stefan Kurtz |
| Platform: |
linux.amd64, linux.x86, solaris.amd64.v10,
solaris.x86.v10, solaris.sparc.v10, solaris.sparc.v10,
osx.amd64, osx.x86, none |
|
| Description: |
REPuter computes all maximal duplications and
reverse, complemented and reverse complemented repeats
in a DNA input sequence. |
| Author(s): |
Stefan Kurtz, Chris Schleiermacher |
| Platform: |
linux.i586, solaris.sparc, solaris.i586,
tru64.alpha, irix.sgi, osx.powerpc |
|
| Description: |
RNA Movies is a system for the visualization of RNA
secondary structure landscapes. Its input is a script
consisting of structures from which animated graphical
structure representations are generated. In this way,
it creates the impression of an RNA-molecule moving
through its own 2D structure space. |
| Author(s): |
Dirk Evers, Alain Xayaphoummine, Hervé
Isambert, Jan Krüger, Alexander Kaiser |
| Platform: |
src, solaris.sparc.opengl, solaris.sparc.mesa,
linux.i586.mesa.xforms0.88, linux.i586.mesa.xforms1.0,
irix.opengl |
| require: |
OpenGL or
Mesa3D and
XForms |
|
| Description: |
RNA Movies is a system for the visualization of RNA
secondary structure landscapes. Its input is a script
consisting of structures from which animated graphical
structure representations are generated. In this way,
it creates the impression of an RNA-molecule moving
through its own 2D structure space. |
| Author(s): |
Dirk Evers, Alain Xayaphoummine, Hervé
Isambert, Jan Krüger, Alexander Kaiser |
| Platform: |
src |
| require: |
OpenGL or
Mesa3D and
XForms |
|
| Description: |
RNA Movies is a system for the visualization of RNA
secondary structure landscapes. Its input is a script
consisting of structures from which animated graphical
structure representations are generated. In this way,
it creates the impression of an RNA-molecule moving
through its own 2D structure space. |
| Author(s): |
Dirk Evers, Alain Xayaphoummine, Hervé
Isambert, Jan Krüger, Alexander Kaiser |
| Platform: |
src |
|
| Description: |
RNA Movies is a system for the visualization of RNA
secondary structure landscapes. Its input is a script
consisting of structures from which animated graphical
structure representations are generated. In this way,
it creates the impression of an RNA-molecule moving
through its own 2D structure space. |
| Author(s): |
Dirk Evers, Alain Xayaphoummine, Hervé
Isambert, Jan Krüger, Alexander Kaiser |
| Platform: |
src |
|
| Description: |
RNA Movies is a system for the visualization of RNA
secondary structure landscapes. Its input is a script
consisting of structures from which animated graphical
structure representations are generated. In this way,
it creates the impression of an RNA-molecule moving
through its own 2D structure space. |
| Author(s): |
Dirk Evers, Alain Xayaphoummine, Hervé
Isambert, Jan Krüger, Alexander Kaiser |
| Platform: |
java, src |
|
| Description: |
RNA Movies is a system for the visualization of RNA
secondary structure landscapes. Its input is a script
consisting of structures from which animated graphical
structure representations are generated. In this way,
it creates the impression of an RNA-molecule moving
through its own 2D structure space. |
| Author(s): |
Dirk Evers, Alain Xayaphoummine, Hervé
Isambert, Jan Krüger, Alexander Kaiser |
| Platform: |
java, src |
|
| Description: |
RNA Movies is a system for the visualization of RNA
secondary structure landscapes. Its input is a script
consisting of structures from which animated graphical
structure representations are generated. In this way,
it creates the impression of an RNA-molecule moving
through its own 2D structure space. |
| Author(s): |
Dirk Evers, Alain Xayaphoummine, Hervé
Isambert, Jan Krüger, Alexander Kaiser |
| Platform: |
java, src |
|
|
|
|
|
|
| Description: |
RNAshapes offers three RNA analysis tools in one
single software package: computation of a small set of
representative structures of different shapes,
computation of shape probabilities, and comparative
prediction of consensus structures. |
| Author(s): |
Bjoern Voss, Peter Steffen, Jens Reeder, Marc
Rehmsmeier, Robert Giegerich |
| Platform: |
src, linux.i586, solaris.i586.v10,
solaris.sparc.v8, win32.i586 |
|
| Description: |
RNAshapes offers three RNA analysis tools in one
single software package: computation of a small set of
representative structures of different shapes,
computation of shape probabilities, and comparative
prediction of consensus structures. |
| Author(s): |
Bjoern Voss, Peter Steffen, Jens Reeder, Marc
Rehmsmeier, Robert Giegerich |
| Platform: |
src, linux.i586, solaris.i586.v10,
solaris.sparc.v8, win32.i586 |
|
| Description: |
RNAshapes offers three RNA analysis tools in one
single software package: computation of a small set of
representative structures of different shapes,
computation of shape probabilities, and comparative
prediction of consensus structures. |
| Author(s): |
Bjoern Voss, Peter Steffen, Jens Reeder, Marc
Rehmsmeier, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32, osx |
|
| Description: |
RNAshapes offers three RNA analysis tools in one
single software package: computation of a small set of
representative structures of different shapes,
computation of shape probabilities, and comparative
prediction of consensus structures. |
| Author(s): |
Bjoern Voss, Peter Steffen, Jens Reeder, Marc
Rehmsmeier, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32, osx |
|
| Description: |
RNAshapes offers three RNA analysis tools in one
single software package: computation of a small set of
representative structures of different shapes,
computation of shape probabilities, and comparative
prediction of consensus structures. |
| Author(s): |
Bjoern Voss, Peter Steffen, Jens Reeder, Marc
Rehmsmeier, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32, osx |
|
| Description: |
RNAshapes offers three RNA analysis tools in one
single software package: computation of a small set of
representative structures of different shapes,
computation of shape probabilities, and comparative
prediction of consensus structures. |
| Author(s): |
Bjoern Voss, Peter Steffen, Jens Reeder, Marc
Rehmsmeier, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32, osx |
|
| Description: |
RNAshapes offers three RNA analysis tools in one
single software package: computation of a small set of
representative structures of different shapes,
computation of shape probabilities, and comparative
prediction of consensus structures. |
| Author(s): |
Bjoern Voss, Peter Steffen, Jens Reeder, Marc
Rehmsmeier, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32, osx |
|
| Description: |
RNAshapes offers three RNA analysis tools in one
single software package: computation of a small set of
representative structures of different shapes,
computation of shape probabilities, and comparative
prediction of consensus structures. |
| Author(s): |
Bjoern Voss, Peter Steffen, Jens Reeder, Marc
Rehmsmeier, Robert Giegerich |
| Platform: |
src, linux.i386, solaris.i386.v10,
solaris.sparc.v8, win32, osx |
|
| Description: |
Searching and classifying non-coding RNAs with Rfam
covariance models is currently considered ideal, but
slow. RNAsifter is a structure-based filtering
technique employing a pre-computed index of structural
abstractions called shapes. Since RNAs are
characterized by structure more than by sequence, our
method is more sensible than sequence-based
filters. |
| Author(s): |
sjanssen, jreeder |
| Platform: |
perl, none, none, none, none |
|
| Description: |
Rococo reconstructs ancestral gene clusters. Given
the topology of a phylogenetic tree and the gene orders
of the leaf nodes, it calculates sets of gene clusters
for the inner nodes preserving consistency and
parsimony. |
| Author(s): |
Roland Wittler |
| Platform: |
java, java, data |
|
| Description: |
ROSE implements a new probabilistic model of RNA-,
DNA-, or protein-sequence evolution. |
| Author(s): |
Jens Stoye, Folker Meyer, Dirk Evers |
| Platform: |
src |
|
| Description: |
Say you are given a permutation of the numbers
1,?,n. The problem is to sort the permutation such that
the numbers are in ascending order. The only operation
you are allowed to perform is a block interchange, that
is, you may take two blocks consisting of consecutive
elements of the permutation and swap them. |
| Author(s): |
Marcel Martin |
| Platform: |
src |
|
| Description: |
SplitsTree uses the split decomposition method to
analyse and visualize distance data, e.g. data derived
from biosequences. See also the original side of
splitstree at the University of Tuebingen. |
| Author(s): |
Daniel Huson |
| Platform: |
src, solaris.sparc, linux.i586, win32.i586 |
| require: |
TCL/TK
V8.05 |
|
| Description: |
SplitsTree uses the split decomposition method to
analyse and visualize distance data, e.g. data derived
from biosequences. See also the original side of
splitstree at the University of Tuebingen. |
| Author(s): |
Daniel Huson |
| Platform: |
mac |
|
| Description: |
The SWIFT suit is a software collection for fast
index-based sequence comparison. It contains the
following programs: SWIFT — fast local alignment
search, guaranteeing to find epsilon-matches between
two sequences; SWIFT BALSAM — a very fast program
to find semiglobal non-gapped alignments based on k-mer
seeds. |
| Author(s): |
Kim Rasmussen, Wolfgang Gerlach |
| Platform: |
solaris.sparc, linux.i586 |
|
| Description: |
The SWIFT suit is a software collection for fast
index-based sequence comparison. It contains the
following programs: SWIFT — fast local alignment
search, guaranteeing to find epsilon-matches between
two sequences; SWIFT BALSAM — a very fast program
to find semiglobal non-gapped alignments based on k-mer
seeds. |
| Author(s): |
Kim Rasmussen, Wolfgang Gerlach |
| Platform: |
src, src |
|
| Description: |
The SWIFT suit is a software collection for fast
index-based sequence comparison. It contains the
following programs: SWIFT — fast local alignment
search, guaranteeing to find epsilon-matches between
two sequences; SWIFT BALSAM — a very fast program
to find semiglobal non-gapped alignments based on k-mer
seeds. |
| Author(s): |
Kim Rasmussen, Wolfgang Gerlach |
| Platform: |
src, src |
|
| Description: |
The SWIFT suit is a software collection for fast
index-based sequence comparison. It contains the
following programs: SWIFT — fast local alignment
search, guaranteeing to find epsilon-matches between
two sequences; SWIFT BALSAM — a very fast program
to find semiglobal non-gapped alignments based on k-mer
seeds. |
| Author(s): |
Kim Rasmussen, Wolfgang Gerlach |
| Platform: |
src, src |
|
| Description: |
The SWIFT suit is a software collection for fast
index-based sequence comparison. It contains the
following programs: SWIFT — fast local alignment
search, guaranteeing to find epsilon-matches between
two sequences; SWIFT BALSAM — a very fast program
to find semiglobal non-gapped alignments based on k-mer
seeds. |
| Author(s): |
Kim Rasmussen, Wolfgang Gerlach |
| Platform: |
src, src |
|
| Description: |
Next-generation sequencing enabled T-cell receptor
(TCR) chain repertoire analysis has gained major
attention in a broad area of clinical and basic
immunological questions. Especially sequencing the beta
chain of the heterodimeric alpha:beta TCR, including
the complementary determining region three (CDR3) which
has been shown to be responsible for antigen
recognition in the immune system's defense mechanisms,
is becoming popular as sequencing costs drop further
and will soon be basic diagnostic routine. However,
despite improvements of sequencing technology, raw data
obtained from next-generation sequencers are usually
prone to errors. Sequencing data from TCRs, including
the hypervariable antigen recognizing CDR3, urge the
need for improved analysis tools, being able to account
for sequencing errors. We developed a tool,
TCRProfiler, including sequencer system specific
quality values to improve reliability of TCR diversity
analysis with the ability to generate probe specific
repertoire profiles, thus enabling to measure patient
specific immunological health status on basis of
measuring timepoint specific CDR3 diversity. |
| Author(s): |
Pina Krell |
| Platform: |
java.1.5, java.1.5, src |
|
| Description: |
TSDA(target site duplication align) is an alignment
tool to analyse recombinant DNA sequences. The program
calculates (local) similarity of two sequences and
shows the optimal alignment(s). The development was
done using the algebraic dynamic programming (ADP)
method. |
| Author(s): |
Daniel Paarmann |
| Platform: |
src |
|
| Description: |
still missing |
| Author(s): |
Julia Herold, Stefan Kurtz, Robert Giegerich |
| Platform: |
src |
|
| Description: |
Wotd is an implementation of the ''lazy''
write-only top-down construction algorithm of suffix
trees using a very space-efficient representation. |
| Author(s): |
Stefan Kurtz |
| Platform: |
src |
|
| Description: |
Wotd is an implementation of the ''lazy''
write-only top-down construction algorithm of suffix
trees using a very space-efficient representation. |
| Author(s): |
Stefan Kurtz |
| Platform: |
src |
|
| Description: |
Wotd is an implementation of the ''lazy''
write-only top-down construction algorithm of suffix
trees using a very space-efficient representation. |
| Author(s): |
Stefan Kurtz |
| Platform: |
src |
|
