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.
A program package to reconstruct phylogenetic trees from protein, DNA, and binary data by maximum likelihood.
A software to simulate and estimate Horizontal Gene Transfer events.
A program to constuct consensus trees from rooted triples.
Next Generation Sequencing
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.
Web-based Automatic Variant (SNPs and INDELs) Identification, Filtering and Annotation of Amplicon Sequencing Data.
An R package developed for the functional analysis of Genome-Wide Association (GWA) studies.
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.
A program for analyzing multiple genome-wide profiling epigenomic data.
A program to rename sequence and taxon names in tree and sequence files.