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 submitted to 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!
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
Source code at AWI-forge
More info...
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!
Download instructions: connect to the ftp server at ftp.awi.de. Log on as "anonymous" with an e-mail address as password. Type "cd pub/EDV", then "get STAMP-v11.zip".
Alternatively: you can get STAMP directly from Christoph Mayer's page.
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
Scilab Numerical Math
Numerical Differentiation
Numerical Integration
Quasi steady state ODE and Heat equation (PDE)