Arndt von Haeseler

The Tetratricopeptide Repeats of Receptors Involved in Protein Translocation across Membranes (2007)

Schlegel, Thomas, Mirus, Oliver, Von Haeseler, Arndt, Schleiff, Enrico

Transport of polypeptides across membranes is a general and essential process in every cell. This process is utilized by molecular machines composed of soluble and membrane-inserted proteins. At...

TreeSnatcher: coding trees from images (2007)

Laubach, Thomas, Von Haeseler, Arndt

Summary: TreeSnatcher is a GUI-driven JAVA application for the semi-automatic recognition of multifurcating phylogenetic trees in pixel images. The program accepts an image file as input and analyzes...

A Likelihood Framework to Measure Horizontal Gene Transfer (2007)

Linz, Simone, Radtke, Achim, Von Haeseler, Arndt

We suggest a likelihood based approach to estimate an overall rate of horizontal gene transfer (HGT) in a simplified setting. To this end, we assume that the number of occurring HGT events within a...

In silico sequence evolution with site-specific interactions along phylogenetic trees (2006)

Gesell, Tanja, Von Haeseler, Arndt

Motivation: A biological sequence usually has many sites whose evolution depends on other positions of the sequence, but this is not accounted for by commonly used models of sequence evolution. Here...

INVHOGEN: a database of homologous invertebrate genes (2006)

Paulsen, Ingo, Von Haeseler, Arndt

Classification of proteins into families of homologous sequences constitutes the basis of functional analysis or of evolutionary studies. Here we present INVertebrate HOmologous GENes (INVHOGEN), a...

HvrBase++: a phylogenetic database for primate species (2006)

Kohl, Jochen, Paulsen, Ingo, Laubach, Thomas, Radtke, Achim, Von Haeseler, Arndt

HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises...

Phylogenetic Diversity within Seconds (2006)

Minh, Bui Quang, Klaere, Steffen, Von Haeseler, Arndt

We consider a (phylogenetic) tree with n labeled leaves, the taxa, and a length for each branch in the tree. For any subset of k taxa, the phylogenetic diversity is defined as the sum of the...

Shortest triplet clustering: reconstructing large phylogenies using representative sets (2005)

Sy Vinh, Le, Von Haeseler, Arndt

Abstract Background Understanding the evolutionary relationships among species based on their genetic information is one of the primary objectives in phylogenetic analysis. Reconstructing phylogenies...

Recent Origin and Cultural Reversion of a Hunter–Gatherer Group (2005)

Oota, Hiroki, Pakendorf, Brigitte, Weiss, Gunter, Von Haeseler, Arndt, Pookajorn, Surin, Settheetham-Ishida, Wannapa, ...

Contemporary hunter–gatherer groups are often thought to serve as models of an ancient lifestyle that was typical of human populations prior to the development of agriculture. Patterns of genetic...

pIQPNNI - parallel reconstruction of large maximum likelihood phylogenies (2005)

Minh, Bui Quang, Vinh, Le Sy, Von Haeseler, Arndt, Schmidt, Heiko A.

Summary: IQPNNI is a program to infer maximum-likelihood phylogenetic trees from DNA or protein data with large number of sequences. We present an improved and MPI-parallel implementation showing...

In silico sequence evolution with site-specific interactions along phylogenetic trees (2005)

Gesell, Tanja, Von Haeseler, Arndt

Motivation: A biological sequence usually has many sites whose evolution depends on other positions of the sequence, but this is not accounted for by commonly used models of sequence evolution. Here...

Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction (2005)

Fleissner, Roland, Metzler, Dirk, Von Haeseler, Arndt

Although the reconstruction of phylogenetic trees and the computation of multiple sequence alignments are highly interdependent, these two areas of research lead quite separate lives, the former...

TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics (2004)

Jobb, Gangolf, Von Haeseler, Arndt, Strimmer, Korbinian

Abstract Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an...

IQPNNI: Moving Fast Through Tree Space and Stopping in Time (2004)

IQPNNI: Moving Fast Through Tree Space and Stopping in Time (2004)

An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a...

IQPNNI: Moving Fast Through Tree Space and Stopping in Time (2004)

An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a...

Identifying site-specific substitution rates (2003)

An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a...

Testing substitution models within a phylogenetic tree (2003)

Nucleotide substitution models (2003)

Phylogeny inference based on maximum-likelihood methods with Tree-Puzzle (2003)

Von Haeseler, Arndt, Strimmer, Korbinian

Population History and Linkage Disequilibrium (2003)

Zöllner, Sebastian, Von Haeseler, Arndt

Maximum-likelihood analysis using TREE-PUZZLE (2003)

Schmidt, Heiko A., Von Haeseler, Arndt

TREE-PUZZLE provides means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e. groups of 4 sequences. Basic Protocol 1 explains how to reconstruct trees based on...

Molecular phylogenetics: parallelized parameter estimation and quartet puzzling (2003)

Schmidt, Heiko A., Petzold, E., Vingron, Martin, Von Haeseler, Arndt

Exponential growth of the data available for molecular sequence analysis causes eminent need for methods to analyze large datasets in reasonable time. In molecular phylogenetics maximum-likelihood...

Testing Substitution Models Within a Phylogenetic Tree (2003)

Identifying site specific substitution rates (2003)

Phylogenetic tree reconstruction frequently assumes the homogeneity of the substitution process over the whole tree. To test this assumption statistically, we propose a test based on the sample...

Testing Substitution Models within a Phylogenetic Tree (2003)

A maximum likelihood framework for estimating site specific substitution rates is presented that does not require any prior assumptions about the rate distribution. We show that the analysis of pairs...

Identifying Site-Specific Substitution Rates (2003)

Phylogenctic tree reconstruction assumes frequently the homogeneity of the substitution process over the whole tree. To test this assumption statistically, we propose a test based on the sample...

Identifying site specific substitution rates (2003)

A maximum likelihood framework for estimating site-specific substitution rates is presented that does not require any prior assumptions about the rate distribution. We show that, when the branching...

Testing Substitution Models within a Phylogenetic Tree (2003)

A maximum likelihood framework for estimating site specific substitution rates is presented that does not require any prior assumptions about the rate distribution. We show that the analysis of pairs...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Phylogenctic tree reconstruction assumes frequently the homogeneity of the substitution process over the whole tree. To test this assumption statistically, we propose a test based on the sample...

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964-969, 1996) that provides...

Territory establishment in lekking marine iguanas, Amblyrhynchus cristatus: support for the hotshot mechanism (2002)

Partecke, J., Von Haeseler, Arndt, Partecke, M.

The territory establishment of male marine iguanas and their subsequent mating success were analysed to identify spatial spillover (hotshot) and temporal spillover effects on lek formation. Males...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, H. A., Strimmer, K., Vingron, M., Von Haeseler, Arndt

TREE-PUZZLE is a program package for quartet-based maximum- likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol Biol. Evol., 13, 964-969, 1996) that provides methods for...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides...

Quartet-Mapping, a Generalization of the Likelihood-Mapping Procedure (2001)

Nieselt-Struwe, Kay, Von Haeseler, Arndt

Likelihood-mapping (LM) was suggested as a method of displaying the phylogenetic content of an alignment. However, statistical properties of the method have not been studied. Here we analyze the...

Pattern of Nucleotide Substitution and Rate Heterogeneity in the Hypervariable Regions I and II of Human mtDNA (1999)

Meyer, Sonja, Weiss, Gunter, Von Haeseler, Arndt

Toward Assigning Helical Regions in Alignments of Ribosomal RNA and Testing the Appropriateness of Evolutionary Models (1999)

Schöniger, Michael, Von Haeseler, Arndt

Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities (1998)

Allen, M., Meyer, Sonja, Handt, O., Saldeen, T., Von Haeseler, Arndt, ...

Compilation of human mtDNA control region sequences (1998)

Handt, O., Meyer, Sonja, Von Haeseler, Arndt

Inference of Population History Using a Likelihood Approach (1998)

Accuracy of Neighbor Joining for n-Taxon Trees (1996)

Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment

A Monte Carlo approach was used to estimate the accuracy of a given tree reconstruction method for any number of taxa. In this procedure, we sampled randomly over all possible bifurcating trees...

TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

We introduce a graphical method, likelihood-mapping, to visualize the phylogenetic content of a set of aligned sequences. The method is based on an analysis of the maximum likelihoods for the three...

Jobb, Gangolf, Von Haeseler, Arndt, Strimmer, Korbinian

Recent Origin and Cultural Reversion of a Hunter–Gatherer Group

Oota, Hiroki, Pakendorf, Brigitte, Weiss, Gunter, Von Haeseler, Arndt, Pookajorn, Surin, Settheetham-Ishida, Wannapa, ...

Contemporary hunter–gatherer groups are often thought to serve as models of an ancient lifestyle that was typical of human populations prior to the development of agriculture. Patterns of genetic...

Shortest triplet clustering: reconstructing large phylogenies using representative sets

Sy Vinh, Le, Von Haeseler, Arndt

HvrBase++: a phylogenetic database for primate species

Kohl, Jochen, Paulsen, Ingo, Laubach, Thomas, Radtke, Achim, Von Haeseler, Arndt

HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises...

INVHOGEN: a database of homologous invertebrate genes

Paulsen, Ingo, Von Haeseler, Arndt

Classification of proteins into families of homologous sequences constitutes the basis of functional analysis or of evolutionary studies. Here we present INVertebrate HOmologous GENes (INVHOGEN), a...

Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment