Software

With EAGER, we provide an intuitive and user-friendly way for researchers to analyse genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data. It offers a pipeline for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.

MUSIAL is a web platform that computes prokaryotic genome, gene and protein sequence alignments 
from variant call datasets (using both SNVs and Indels) derived from multiple samples of one species. 

Interactive visual analytics tool for the simultaneous exploration of phylogenetic relationships, genome-wide SNP data and metadata.

BLASTphylo is an interactive web-tool, which applies a BLASTp search for a given protein and maps the result on a given taxonomic tree. In addition, a phylogeny calculation of the remaining BLAST hits can be performed and visualized.

An interactive visualization tool for the integration of proteomics and transcriptomics data. The tool consists of an automated part that clusters omics data to determine trends in the combined data sets and an interactive visualization.

Comparative visualization of GO enrichments results from multiple lists of genes.

DeSEQ2-Vis

An R-shiny app that allows interactively using the DeSeq2 R package in a user-friendly web app without any programming expertise.

Visualization approach for the exploration of small-world networks in conjunction with metadata, such as Protein Protein Interaction (PPI) networks combined with pathway annotations.

GenomeRing

Whole genome alignment visualization based on SuperGenome coordinates. Whole-genome alignments elucidate similarity and diversity on different scales, GenomeRing highlights both similarity and variation of the genome architecture of a species. Its is mainly developed for bacterial genomes.

TSSpredator

Comparative Transcription Start Site (TSS) prediction from RNA-seq data and enriched datasets.

nocoRNAc

nocoRNAc is a software for the automated prediction and characterization of ncRNA transcripts in bacterial genomes.

TSS-Captur

TSS-Captur characterizes transcripts starting on clear TSS signals obtained from TSSpredator that cannot be associated with any known gene. To characterize the function of the transcript, TSS-Captur integrates tools using different approaches.

VIPurPCA offers a visualization of uncertainty propagated through the dimensionality reduction technique Principal Component Analysis (PCA) by automatic differentiation.

Mayday is a microarray data analysis platform and is designed to be a flexible solution for processing microarray data. It features interactive visualization as well as a plug-in framework to support analytical tools.

GPA

Our Genome Profile Alignment tool GPA relies on progressiveMauve for the underlying alignment, to compute several smaller sets of aligned genomes that are combined to a full WGA through their profiles. The computation of the profiles of the WGAs and their merging is conducted by using the SuperGenome data structure.

MADAM

Improving Ancient DNA Assembly

InPHAP

inPHAP is our interactive phased haplotype visualization tool, featuring a variety of interaction possibilities such as zooming, sorting, filtering and aggregation of rows in order to explore patterns hidden in large genetic datasets.

PanGee

PanGee is a software tool that computes the PanGenome from a given whole genome alignment (WGA). The computation refines homologous genes groups through a subsequent Reciprocal Best Hit-BLAST approach.  For this, we make use of the SuperGenome data structure that offers the possibility to efficiently detect aligned homologs in the WGA.

Pan-Tetris

Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game.