BiBiServ Software Download
BiBiServ

BiBiServ Software Download

This is a list of all packages distributed via the BiBiServ software download section.

AggloDel

1.0

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

AIM

0.81

Description:Automatic Image processing for Microarrays
Author(s):Mathias Katzer
Platform:linux.i586.glibc61, linux.i586.glibc62

AIM

0.82

Description:Automatic Image processing for Microarrays
Author(s):Mathias Katzer
Platform:linux.i586

bpr

0.9.0 and 2.0.0

Description:Bpr is an implementation of the 'bucket-pointer refinement' construction algorithm for suffix arrays
Author(s):Klaus-Bernd Schrmann, Jens Stoye
Platform:src, src, none, none

DCA

1.1

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

DIALIGN

2.2.1

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

Gecko

1.1

Description:Gene cluster detection in prokaryotic genomes
Author(s):Katharina Jahn and Leon Kuchenbecker
Platform:java.1.4

Gecko

1.2

Description:Gene cluster detection in prokaryotic genomes
Author(s):Katharina Jahn and Leon Kuchenbecker
Platform:java.1.4

Gecko

1.2.1

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

Gecko

2.0

Description:Gene cluster detection in prokaryotic genomes
Author(s):Katharina Jahn and Leon Kuchenbecker
Platform:java.1.6

GUUGle

1.0

Description:A utility for fast exact matching under RNA base pairing rules
Author(s):Wolfgang Gerlach
Platform:src

GUUGle

1.1

Description:A utility for fast exact matching under RNA base pairing rules
Author(s):Wolfgang Gerlach
Platform:src

GUUGle

1.2

Description:A utility for fast exact matching under RNA base pairing rules
Author(s):Wolfgang Gerlach
Platform:src

InSilicoDicer

1.0

Description:Intrinsic and Extrinsic Prediction of mature miRNA.
Author(s):Sylvia Tippmann, Jan Krueger
Platform:java

InSilicoDicer

1.1

Description:Intrinsic and Extrinsic Prediction of mature miRNA.
Author(s):Sylvia Tippmann, Jan Krueger
Platform:java

JALI

1.3

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

JPREdictor

0.9

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

JPREdictor

1.0

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

JPREdictor

1.05

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

JPREdictor

1.1

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

JPREdictor

1.101

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

JPREdictor

1.13

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

JPREdictor

1.14

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

JPREdictor

1.2

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

JPREdictor

1.21

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

JPREdictor

1.22

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

JPREdictor

1.23

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

libfid

0.2.4

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

libfid

0.2.6

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

libfid

0.3.0

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

libfid

0.3.1

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

libfid

0.3.1a

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

libfid

0.3.2

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

libfid

0.4.0

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

libfid

0.4.1

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

MGA

2003-03-18

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

mkESA

1.0

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

mkESA

1.0.1

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

mkESA

1.0.2

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

mkESA

1.0.4

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

OMA

0.98

Description:Optimal Multiple Sequence Alignment
Author(s):Thorsten Will, Knut Reinert, Jens Stoye
Platform:src

OMA

1.0

Description:Optimal Multiple Sequence Alignment
Author(s):Thorsten Will, Knut Reinert, Jens Stoye
Platform:solaris.sparc

Paper2Sequence

0.85

Description:Simple retrieval of sequences
Author(s):Henning Mersch, Georg Fuellen
Platform:src

Phase4

1.6

Description:Automatic evaluation of database search methods.
Author(s):Marc Rehmsmeier
Platform:src

pknotsRG

1.0

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

pknotsRG

1.1

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

pknotsRG

1.2

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

pknotsRG

1.3

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

planACstar

1.0

Description:planACstar is an implementation of plan AC* that improves structural RNA alignments by structure comparison
Author(s):Andreas Bremges
Platform:src
require:BioPerl

planACstar

1.1

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

PoSSuMsearch

1.0

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

PoSSuMsearch

1.2

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

PoSSuMsearch

1.2a

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

PoSSuMsearch

1.3

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

PoSSuMsearch2

2.0

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

REPuter

2.74

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

RNA Movies

1.0

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, Herv Isambert, Jan Krger, 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

RNA Movies

1.2

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, Herv Isambert, Jan Krger, Alexander Kaiser
Platform:src
require:OpenGL or
Mesa3D and
XForms

RNA Movies

2.0

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, Herv Isambert, Jan Krger, Alexander Kaiser
Platform:src

RNA Movies

2.01

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, Herv Isambert, Jan Krger, Alexander Kaiser
Platform:src

RNA Movies

2.02

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, Herv Isambert, Jan Krger, Alexander Kaiser
Platform:java, src

RNA Movies

2.03

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, Herv Isambert, Jan Krger, Alexander Kaiser
Platform:java, src

RNA Movies

2.04

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, Herv Isambert, Jan Krger, Alexander Kaiser
Platform:java, src

RNAforester

1.4

Description:RNA Forester is an alignment tool for RNA secondary structures. It is suitable for global comparision of RNA secondary structures and for finding similar regions between them.
Author(s):Matthias Hoechsmann
Platform:src
require:G2 library (for graphical output)
GD library (for graphical output)

RNAforester2

2.0

Description:RNA Forester is an alignment tool for RNA secondary structures. It is suitable for global comparision of RNA secondary structures and for finding similar regions between them.
Author(s):Stefanie Schirmer
Platform:src
require:G2 library (for graphical output)
GD library (for graphical output)

RNAhybrid

1.0

Description: RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA.
Author(s):Marc Rehmsmeier, Matthias Hoechsmann, Peter Steffen
Platform:src
require:G2 (optional PS support) and
GD (for additionally PNG/JPEG support)

RNAhybrid

2.0

Description: RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA.
Author(s):Marc Rehmsmeier, Matthias Hoechsmann, Peter Steffen
Platform:src
require:G2 (optional PS support) and
GD (for additionally PNG/JPEG support)

RNAhybrid

2.1

Description: RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA.
Author(s):Marc Rehmsmeier, Matthias Hoechsmann, Peter Steffen
Platform:src, osx, win32
require:G2 (optional PS support) and
GD (for additionally PNG/JPEG support)

RNAhybrid

2.1.1

Description: RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA.
Author(s):Marc Rehmsmeier, Matthias Hoechsmann, Peter Steffen
Platform:src, linux, linux, osx, win32
require:G2 (optional PS support) and
GD (for additionally PNG/JPEG support)

RNAshapes

1.0

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

RNAshapes

1.1

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

RNAshapes

2.0

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

RNAshapes

2.0.1

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

RNAshapes

2.1

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

RNAshapes

2.1.1

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

RNAshapes

2.1.5

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

RNAshapes

2.1.6

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

RNAsifter

1.0

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

Rococo

2.0

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

ROSE

1.3

Description:ROSE implements a new probabilistic model of RNA-, DNA-, or protein-sequence evolution.
Author(s):Jens Stoye, Folker Meyer, Dirk Evers
Platform:src

SBBI

1.0

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

SplitsTree

3.2

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

SplitsTree

2.4

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

SWIFT suit

1.0

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

SWIFT suit

1.0.1

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

SWIFT suit

1.1

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

SWIFT suit

1.2

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

SWIFT suit

1.3

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

TCRProfiler

1.0

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

TCRProfiler

1.1

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

TSDA

1.0

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

UniMoG (former DCJ)

1.0

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

unwords

1.0

Description:still missing
Author(s):Julia Herold, Stefan Kurtz, Robert Giegerich
Platform:src

Wotd

1.0

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

Wotd

1.1

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

Wotd

1.11

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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