This is a list of all packages distributed via the BiBiServ
software download section.
| Description: | This tool to detect structural variations is specifically designed to cluster short-read paired-end data into possibly overlapping deletion predictions. The method does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity, polyploidy, etc. Taking paired ends mapped to a reference genome as input, it iteratively merges mappings to clusters based on a similarity score that takes both the putative location and size of a deletion into account. | | Author(s): | Roland Wittler | | Platform: | java.1.6, none |
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| Description: | Automatic Image processing for Microarrays | | Author(s): | Mathias Katzer | | Platform: | linux.i586.glibc61, linux.i586.glibc62 |
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| Description: | Automatic Image processing for Microarrays | | Author(s): | Mathias Katzer | | Platform: | linux.i586 |
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| 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 |
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| 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 |
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| 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 |
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| Description: | Gene cluster detection in prokaryotic genomes | | Author(s): | Katharina Jahn and Leon Kuchenbecker | | Platform: | java.1.4 |
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| Description: | Gene cluster detection in prokaryotic genomes | | Author(s): | Katharina Jahn and Leon Kuchenbecker | | Platform: | java.1.4 |
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| 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 |
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| Description: | Gene cluster detection in prokaryotic genomes | | Author(s): | Katharina Jahn and Leon Kuchenbecker | | Platform: | java.1.6 |
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| Description: | A utility for fast exact matching under RNA base pairing rules | | Author(s): | Wolfgang Gerlach | | Platform: | src |
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| Description: | A utility for fast exact matching under RNA base pairing rules | | Author(s): | Wolfgang Gerlach | | Platform: | src |
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| Description: | A utility for fast exact matching under RNA base pairing rules | | Author(s): | Wolfgang Gerlach | | Platform: | src |
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| Description: | Intrinsic and Extrinsic Prediction of mature miRNA. | | Author(s): | Sylvia Tippmann, Jan Krueger | | Platform: | java |
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| Description: | Intrinsic and Extrinsic Prediction of mature miRNA. | | Author(s): | Sylvia Tippmann, Jan Krueger | | Platform: | java |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| Description: | Optimal Multiple Sequence Alignment | | Author(s): | Thorsten Will, Knut Reinert, Jens Stoye | | Platform: | src |
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| Description: | Optimal Multiple Sequence Alignment | | Author(s): | Thorsten Will, Knut Reinert, Jens Stoye | | Platform: | solaris.sparc |
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| Description: | Simple retrieval of sequences | | Author(s): | Henning Mersch, Georg Fuellen | | Platform: | src |
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| Description: | Automatic evaluation of database search methods. | | Author(s): | Marc Rehmsmeier | | Platform: | src |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| Description: | planACstar is an implementation of plan AC* that improves structural RNA alignments by structure comparison | | Author(s): | Andreas Bremges | | Platform: | src | | require: | BioPerl |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| Description: | ROSE implements a new probabilistic model of RNA-, DNA-, or protein-sequence
evolution. | | Author(s): | Jens Stoye, Folker Meyer, Dirk Evers | | Platform: | src |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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.1.6 |
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| 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 |
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| Description: |
UniMoG is a software tool unifying four genome rearrangement distance models: double cut and join (DCJ), Hannenhalli and Pevzner (HP), inversion only and translocation only. It allows
computing all of these four distances between pairs of genomes. Furthermore, an optimal sorting scenario transforming the first genome of the pair into the second one is returned. All four models make use of the classical rearrangement operations and both linear and circular chromosomes can be handled dependent on the model. NOTE: The old DCJ tool is still available here, too. | | Author(s): | Rafael Friesen, Rolf Hilker | | Platform: | java.1.6, src |
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| Description: | still missing | | Author(s): | Julia Herold, Stefan Kurtz, Robert Giegerich | | Platform: | src |
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| 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 |
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| 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 |
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| 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 |
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