Software

PhyloAssigner

PhyloAssigner is a Perl pipeline for phylogenetic classification of amplicon pyrosequences. For details, see

Kevin L Vergin, Bánk Beszteri, Adam Monier, J Cameron Thrash, Ben Temperton, Alexander H Treusch, Fabian Kilpert, Alexandra Z Worden and Stephen J Giovannoni: High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences. ISME J. doi:10.1038/ismej.2013.32

The pipeline is available for use on LINUX systems and can be downloaded here. This distribution package also contains two marine microbial SSU rDNA reference databases. Up-to-date development version of the source code is available in a subversion repository on awi-forge.

Please read the escape clause on the right hand side before downloading!


MCL-LOvE - Markov-clustering for Library Overlap Estimation

This tool was designed by S. Frickenhaus. It was used in the preparation of the article:

Harms L, Frickenhaus S, Schiffer M, Mark FC, Storch D, Pörtnera HO, Held C, Lucassen M. (2013) Characterization and analysis of a transcriptome from the boreal spider crab Hyas araneus. Comparative Biochemistry and Physiology: Part D: Genomics and Proteomics

Here you get access to the MCL-clustering scripts written in R to perform an overlap-calculation of three EST-sequence-libraries from a tblastx run.

PLEASE READ THE ESCAPE CLAUSE ON THE RIGHT HAND SIDE BEFORE DOWNLOAD!

The example data is a random subset of the orignial data. Hyas Sequence names have been renamed. For complete re-run you need a Linux computer with "mcl" and "ncbi-blast+" packages installed; tested on Ubuntu 12.04.1 LTS. The main R-script requires the R-package seqinr. It produces two Venn diagrams, one summarizing the amounts of clusters that share sequences between different libraries and one summarizing the numbers of sequences within these clusters.


Alignancer

This is the download-link for Alignancer, a python program to align unaligned regions in a HMMer-3 output alignments, written by Fabian Kilpert.


CorNet correlation network graphs

R-script largest correlation network graphs for visualizing clusters of intercorrelated genes/transcripts

Supplpemntal code to the manuscript

Impacts of seawater acidification on mantle gene expression patterns   of the Baltic Sea blue mussel: implications for shell formation and energy budget.  (2012),  Hüning AK, Melzner F, Thomsen J, Gutowska MA, Krämer L, Frickenhaus S, Rosenstiel P, Pörtner HO, Philipp E, Lucassen M, Marine Biology


PhylochipAnalyzer

The PhylochipAnalyzer is a Windows-program for the analysis of experiments with hierarchical probe-sets. It operates in two modes: first, the hierarchy of probes is defined interactively, second, the intensity data of a hybridized chip is loaded and analyzed according to the hierarchy. The program can export hierarchy trees to Newick-format and analyzed data to Excel. It contains a Delphi-script that makes it configurable with respect to different criteria for positive signals.

Reference

Metfies K, Borsutzki P, Gescher C, Medlin LK, Frickenhaus S 

Phylochipanalyser — a program for analysing hierarchical probe sets

Molecular Ecology Resources (2008) 8, 99–102

doi:10.1111/j.1471-8286.2007.01927.x

PLEASE READ THE ESCAPE CLAUSE ON THE RIGHT HAND SIDE BEFORE DOWNLOAD!
Download PhylochipAnalyzer-1

Download UserGuide (pdf)

Contact

Prof. Dr. Stephan Frickenhaus
Dr. Bánk Beszteri
Dipl. Bioinf. Stefan Neuhaus

Former developers:

Philipp Borsutzki
Lars Kraemer
Stefan Pinkernell

Escape clause for downloadable software from the AWI Bioinformatics Group

THE SOFTWARE FROM THE BIOINFORMATICS GROUP AT AWI IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL AWI OR ITS STAFF BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

PhyloGena

PhyloGena is a java application to aid in the phylogenetic annotation of multiple sequences, developed by Kristian Hanekamp. The program performs BLAST searches for the query (protein or DNA) sequences and selects a meaningful subset of them, which it uses for construction of multiple alignments and phylogenetic trees.  The BLAST results, selections, multiple alignments and phylogenetic trees can be viewed by the user in an interactive manner. Different databases, multiple alignment and phylogenetic analysis programs can be plugged into the software.

Reference
Hanekamp, K., Bohnebeck, U., Beszteri, B., Valentin, K. (2007). PhyloGena – a user-friendly system for automated phylogenetic annotation of unknown sequences, Bioinformatics 23: 793-801,
doi: 10.1093/bioinformatics/btm016.

PLEASE READ THE ESCAPE CLAUSE ON THE RIGHT HAND SIDE BEFORE DOWNLOAD!
Download phylogena1.04.zip

Phylogena manual

More info...

Phylogena

STAMP: Microsatellite marker design extension for the Staden package

A Staden package extension for automating microsatellite marker design was developed by Lars Kraemer (now IKMB Kiel). It integrates the de novo repeat identification program Phobos by Christoph Mayer and PRIMER3 into Pregap and Gap4. It allows tagging repeats for masking them out for assembly (Pregap), finding repeats in assembled Gap4 databases, automatic primer design flanking marked repeats and multiplex primer design. The extensions are available as complete packages for Windows, Linux and OS-X.

Reference

Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K. & Frickenhaus, S. (2009) STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.

PLEASE READ THE ESCAPE CLAUSE ON THE RIGHT HAND SIDE BEFORE DOWNLOAD!

You can get STAMP directly from Christoph Mayer's page or from AWI here.

Quicktree-SD

We recently implemented scroredist distances [Sonnhammer and Hollich, Bioinformatics 6:108] in quicktree, a program for fast phylogenetic tree construction from multiple alignments [Howe et al., Bioinformatics 18: 1546]. The software is available now and here. Please cite as

Frickenhaus, S., Beszteri, B. (2008), Quicktree-SD, Software developed by AWI-Bioinformatics, http://hdl.handle.net/10013/epic.33164


HDF4-HDF5-Converter

Here we give for download a cygwin-compiled HDF-converter.

Sparadoxa-primertable