|
|
-
Tancred Frickey & Georg Weiller
CLANS is a program that uses a self-organizing map to display datasets of pairwise relationships. It was originally developed to detect families of related proteins in large sets of sequences, but has since been extended to include microarray analysis capabilities and provide a quick and easy way to compare expression data to functional annotation or cellular localization.
CLANS is a Java program and should run mith minimal hassle on most computers. Only prerequisite is that a Java1.5 or better runtime environment be available (which you can download HERE)
The program is available for free download under the GNU-GPL HERE; source code is included in the archive.
A short help is available HERE
as well as a tutorial HERE.
-
Tancred Frickey & Andrei Lupas
PhyloGenie consists of a set of perl and java programs that allow fully automated generation and semi-automated analysis of phylomes (i.e. the set of phylogenetic trees derived for all proteins in a genome).
PhyloGenie should run mith minimal hassle on most computers. Only prerequisite is that PERL and a Java1.5 or better runtime environment be available
The program is available for free download under the GNU-GPL HERE; source code for the java programs is included in the archives.
-
Tancred Frickey
AlnEdit was born from the need to manually inspect and edit multiple sequence alignments containing thousands of sequences (and not being able to find any editors being able to do that)
AlnEdit is a Java program and should run mith minimal hassle on most computers. Only prerequisite is that a Java1.5 or better runtime environment be available (which you can download HERE)
The program is available for free download under the GNU-GPL HERE; source code is included in the archive.
-
Tancred Frickey & Georg Weiller
BlatView maps results from a BLAT search on to the corresponding genome/chromosome/BAC clones.
BlatView is a java program and should run mith minimal hassle on most computers. Only prerequisite is that a Java1.5 or better runtime environment be available (which you can download HERE
The program is available for free download under the GNU-GPL HERE; source code is included in the archives.
-
Tancred Frickey
JTreeView is a basic tree viewer that lets you view, reroot, rotate nodes and edit further aspects of New Hampshire bracket format trees.
JTreeView is a Java program and should run mith minimal hassle on most computers. Only prerequisite is that a Java1.5 or better runtime environment be available (which you can download HERE)
The program is available for free download under the GNU-GPL HERE; source code is included in the archive. An applet version is available HERE
-
Tancred Frickey & Johannes Soeding
HMMAccel is a small perl scipt that combines PSIBLAST with HMM-searches and greatly increases the speed of the latter.
The program is available for free download under the GNU-GPL HERE
-
Tancred Frickey & Georg Weiller
SSalign takes a DNA/RNA sequence and attempts to determine all local alignments a sequence can produce with itself. In addition, it resolves the little problem that aligning sequences using the standard smith-waterman approach can produce different results depending from which side the alignment matrix is filled.
SSalign is a Java program and should run mith minimal hassle on most computers. Only prerequisite is that a Java1.5 or better runtime environment be available (which you can download HERE)
The program is available for free download under the GNU-GPL HERE; source code is included in the archive.
-
Tancred Frickey & Andrei Lupas
Automated analysis of phylogenetic trees is far more complex than analysis of, for example, pairwise similarities such as calculated by BLAST or PSIBLAST. For the phylome inference package "PhyloGenie" to be regarded as useful, there has to be a way to separate relevant from irrelevant trees for the question at hand.
PHAT (Phylome Analysis Tool) is a tool that filters a set of Newick trees (New Hampshire Bracket Format) for those corresponding to topological selection criteria. Careful choice of the selection criteria can greatly reduce the number of trees that have to be manually examined.
Phat should run mith minimal hassle on most computers. Only prerequisite is that PERL and a Java1.6 or better runtime environment be available
The program is part of the PhyloGenie package, available for free download under the GNU-GPL HERE; source code for the java programs is included in the archives.
-
Tancred Frickey & Georg Weiller
Mclip is a tool for motif-elucidation in DNA/RNA-sequences. Although there are a large number of motif-detection tools around, most require "nuisance" parameters to be specified (i.e. things you would like the program to tell you, not the other way around), such as the exact width of the motif you are searching for, or how often it will be present in the set of sequences you supplied.
Quite a few program will also return the best motif only, without any estimate of how good the second best would have been, or provide cryptic statistical estimates for the "quality" of detected motifs.
Mclip uses a deterministic, expectation-maximization approach to motif detection that can find gapped motifs and provides a P-value or E-value estimate for each motif found in a sequence.
Mclip is a Java program and should run mith minimal hassle on most computers. Only prerequisite is that a Java1.5 or better runtime environment be available (which you can download HERE)
The program is available for free download under the GNU-GPL HERE; source code is included in the archive.
For motif detection in small sets of sequences a web-interface is available HERE
Further information is available HERE
|
