Software developed at the Department

• ALIFRITZ
  performs statistical multiple alignment and phylogeny reconstruction simultaneously.
  The package is available at the ALIFRITZ homepage.

• DAGwoman - DAG-based WOrkflow MANager
  is a workflow engine that allows running and managing DAG-based scientific workflows on computing resources.
  The package is available at the DAGwoman homepage.

• EMOGEE (Estimator for MOdels of Gene Expression Evolution)
  implements neutral models for evolution of gene expression to analyze or simulate microarray data.
  EMOGEE and related tools are available at the EMOGEE homepage.

• Epi-Speller
  is a program for analyzing multiple genome-wide profiling epigenomic data.
  The package is available at the Epi-Speller homepage

• GeoMeTree (Geodesic Metric on Trees)
  GeoMeTree is a python program to compute the geodesic path between two phylogenetic trees.
  The package is available at the GeoMeTree homepage.

• HaMSTR
  HaMSTR is 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. HaMSTR is accessible at www.deep-phylogeny.org/hamstr.

• HGT
  A software to simulate and estimate Horizontal Gene Transfer events.
  The package is available at the HGT homepage.

• 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. ImOSM homepage.

• IQPNNI (Important Quartet Puzzling with NNI Optimization)
  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.
  The package is available at the IQPNNI homepage.

• IQ-TREE (Efficient reconstruction of large maximum-likelihood phylogenies)
  An efficient maximum likelihood algorithm for phylogenetic tree reconstruction and an ultra-fast approximation for phylogenetic bootstrap.
  The package is available at the IQ-Tree homepage.

• MASon (Million Alignments in Seconds)
  is a C++ library that uses high performance architectures to reduce the computing time of NGS analysis pipelines.
  The program is available at the MASon homepage.

• misfits
  is a computer program to evaluate the goodness of fit between a phylogenetic model and an alignment.
  The program is available at the misfits homepage.

• MRC.py
  is a computer program to evaluate the compatibility lengths given supertrees and gene trees and to extract the supertrees with the minimal lengths.
  The program is available at the MRC homepage.

• NextGenMap (Next Generation Mapper)
  is a computer program to map NGS reads against a reference genome using CPUs or GPUs.
  The program is available at the NextGenMap homepage.

• NGC
  A compressor for high-throughput sequencing data.
  The package is available at the NGC homepage.

• NGV (Next Generation Viewer)
  A Preprocessor and Browser for efficient display of large HTS Data Sets.
  The package is available at the NGV homepage.

• Parat
  estimates site specific substitution rates from a set of DNA sequences.
  The package is available at the Parat homepage.

• PDA (Phylogenetic Diversity Algorithm)
  implements efficient algorithms to solve the Phylogenetic Diversity (PD) problem.
  The package is available at the PDA homepage.

• PhyNav (Phylogenetic Navigator)
  A tree sampling method to reconstruct phylogenetic trees from really large datasets (DNA and protein). The method combines different methods to sample good trees.
  PhyNav homepage.

• (p)IPHULA [(parallel) Inference of Population History Using a Likelihood Approach]
  (p)IPHULA is a software that investigates parameters of population history based on a Monte Carlo simulation using the maximum likelihood framework.
  IPHULA/pIPHULA homepage.

• PluMiST - Plus and Minus SuperTrees
  PluMiST is a computer program to reconstruct and evaluate majority rule supertrees: MR(-), MR(+) and MR(+)g.
  The software is available at the PluMiST homepage.

• RecDetec - detecting recombination and phylogenetic information along alignments
  RecDetec is 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.
  The package is available at the RecDetec homepage.

• REvolver: Modeling sequence evolution under domain constraints
  REvolver is a program to simulate protein sequence evolution. REvolver automatically integrates domain information described by a profile Hidden Markov Model (pHMM) into the simulation.
  The package is available at the REvolver homepage.

• Shortest Triplet Clustering (STC)
  A new distance-based clustering method to reconstruct very large phylogenies in polynomial time O(n^2) for n sequences.
  The package is available at the STC homepage.

• SIMULATOR
  Software to simulate DNA and protein datasets with well-defined insertion-deletion dynamics according to a user-given tree.
  The software is available at the SIMULATOR homepage.

• SISSI (Simulating Sequence Evolution with Site-Specific Interactions)
  SISSI is 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.
  The software is available at the SISSI homepage.

• SNP2GO
  is an R package developed for the functional analysis of Genome-Wide Association (GWA) studies. The package is available at the SNP2GO homepage.

• TAXNAMECONVERT
  is a program to rename sequence and taxon names in tree and sequence files.
  The software is available at the Taxnameconvert homepage.

• TREE-PUZZLE
  is a program package to reconstruct phylogenetic trees from protein, DNA, and binary data by maximum likelihood.
  The package is available at www.tree-puzzle.de.

• TreeSnatcher
  is a GUI-driven Java application that recognizes bifurcating and multifurcating trees in pixel images (like JPG) and outputs the tree in Newick format.
  The software is available at the TreeSnatcher homepage.

• TripleC
  a program to constuct consensus trees from rooted triples.
  The software is available at the TripleC homepage.