amplikyzer: a  BS-seq amplicon analyzer

Sven Rahmann

Next-generation sequencing technologies that produce flowgrams (in .sff format) are used to sequence amplicons from different samples or patients. The "amplikyzer" tool helps with the analysis of amplicon reads, especially for methylation studies together with bisulfite sequencing.
Source code is available from the amplikyzer google code homepage (MIT License).
The software is still in pre-alpha stage; no recommended download is available yet. The APIs may still change.

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Protein Hypernetworks

Johannes Köster

This software will accompany our submitted "Protein Hypernetworks" paper once it is published.
The license is to be determined.
For access to our predictions, please see the Protein Hypernetworks research page.

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StyPyl

Sven Rahmann

StylPyl is a command line utility that will scan an input file (typically a .tex or .txt file) for certain patterns that indicate bad writing style (e.g., according to Strunk and White's classic "The Elements of Style"). The stylpyl executable comes with a large number of typical patterns from the author's experience in writing computer science and bioinformatics papers. Custom patterns can be added by each user as stylpyl library files.
Source code is available from the stylpyl google code homepage (MIT License).
The software is in beta stage and especially useful for shortening papers without removing content.

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Motif Statistics and Discovery (MoSDi)

Tobias Marschall

The MoSDi software package contains several sequence analysis algorithms, including methods for

1. motif statistics, e.g. compute the exact occurrence count distribution of a motif,
2. exact motif discovery: extraction of motifs with provably optimal p-value,
3. analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text (see Research page).

Distributed under the GPL. Visit the MoSDi hompage for more details.

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Cutadapt: Remove adapter sequences from high-throughput sequencing reads

Marcel Martin
See the cutadapt Google code homepage.

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Horspool-Analyser (DEPRECATED, use MoSDi instead)

Tobias Marschall
This software accompanies our LATA'10 paper (see Research): a JAVA program to compute the exact distribution of character accesses by Horspool's and Sunday's pattern matching algorithms. The code has been included into MoSDi (see above). However, you may still download this package to easily reproduce the results from our LATA'10 paper.
Source code: horspool-analysis-source.tar.gz
Distributed under the GPL.

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LogoMat-M

Benjamin Schuster-Böckler, Sven Rahmann
Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. We present a method to visualize all of their central aspects graphically, thus generalizing the concept of sequence logos introduced by Schneider and Stephens. For each emitting state of the pHMM, we display a stack of letters. As for sequence logos, the stack height is determined by the deviation of the position's letter emission frequencies from the background frequencies of the letters. As a new feature, the stack width now visualizes both the probability of reaching the state (the hitting probability) and the expected number of letters the state emits during a pass through the model (the expected contribution). [Publication] [Software]

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Further Software (not yet sorted)

• VerJInxer
• Promide / LOligoD
• REFORM
  
• Multinomial
  
• Parrondo Paradoxon