Software

Phylogenetics Inference

IQ-TREE - Efficient phylogenomic inference

Efficient tree reconstruction for phylogenomic data, ultrafast approximation for phylogenetic bootstrap, ultrafast model selection. IQ-TREE supports a wide range of evolutionary models and high performance computing.

TREE-PUZZLE

A program package to reconstruct phylogenetic trees from protein, DNA, and binary data by maximum likelihood.

IQPNNI - Important Quartet Puzzling and Nearest Neighbor Interchange

A quartet based method to reconstruct phylogenetic trees from really large datasets (DNA and protein). The method applies a QP-like approach requiring only a part of the quartets and some fast NNI optimization.

PDA - Phylogenetic Diversity Analyzer

Efficient algorithms to solve the Phylogenetic Diversity (PD) problem.

HGT

A software to simulate and estimate Horizontal Gene Transfer events.

TripleC

A program to constuct consensus trees from rooted triples.

Next Generation Sequencing

NextGenMap - Next Generation Mapper

A computer program to map NGS reads against a reference genome using CPUs or GPUs.

Teaser

A software package for optimizing NGS read mapping results. Through rapid automated benchmarks on simulated or real data sets, the most suitable mapper for an experiment can be found within minutes. By testing the same mapper on multiple parameter settings, results can be further tuned for accuracy or speed. At the end of each benchmark, Teaser presents the results in a browser-viewable report that includes interactive figures.

TRUmiCount - Correctly counting molecules using UMIs

For NGS experiments using unique molecular identifiers (UMIs), molecules that are lost entirely during sequencing cause under-estimation of the molecule count, and amplification artifacts like PCR chimeras cause over-estimation. TRUmiCount corrects UMI data for both types of errors, thus improving the accuracy of measured molecule counts considerably.

iPoolSeq Pipeline - Analyse insertion pool sequencing data

The iPool-Seq analysis pipeline is based on the TRUmiCount algorithm (Pflug et al. 2018) for the quantitative analysis of UMI data, and takes are of all steps of the analysis of iPool-Seq data. From from raw sequencing reads it computes the differential virulences of the mutants in the pre-infection pool compared to a set of reference mutants.

VARIFY

Web-based Automatic Variant (SNPs and INDELs) Identification, Filtering and Annotation of Amplicon Sequencing Data.

NGC - A compressor for high-throughput sequencing data

A compressor for high-throughput sequencing data.

BiSS - Bisulfite Sequencing Scrorer

An analysis pipeline for the deep sequencing data after bisulfite conversion (BS-Seq).

MASon - Million Alignments in Seconds

A C++ library that uses high performance architectures to reduce the computing time of NGS analysis pipelines.

SNP2GO

An R package developed for the functional analysis of Genome-Wide Association (GWA) studies.

Phylogenetics Modelling

HaMSTR

A Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes.

ImOSM - Imbed One Step Mutations into an alignment

A program to Imbed model violation as One Step Mutations into a sequence alignment. This is a useful tool to study the robustness in phylogeny inference.

MISFITS - Evaluating the goodness of fit between a phylogenetic model and an alignment

A computer program to evaluate the goodness of fit between a phylogenetic model and an alignment.

ALIFRITZ - Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction

A program performing statistical multiple alignment and phylogeny reconstruction simultaneously.

SISSI - Simulating Sequence Evolution with Site-Specific Interactions

A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices.

DupliDeli - Estimation of Gene Family Specific Duplication and Deletion Rates

A program to estimate gene family specific duplication and deletion rates as well as the ancestral number of gene copies.

RecDetec - detecting recombination and phylogenetic information along alignments

A software to investigate recombination scenarios based on the bootscan principle along alignments of (viral) genomes. It also allowes to assess the content of phylogenetic information along alignments.

REvolver - Modeling sequence evolution under domain constraints

A program to simulate protein sequence evolution. REvolver automatically integrates domain information described by a profile Hidden Markov Model (pHMM) into the simulation.

Software developed at the Department