Heiko A Schmidt
Affiliation: Max Planck Institute for Evolutionary Anthropology
- Maximum-likelihood analysis using TREE-PUZZLEHeiko A Schmidt
Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Vienna, Austria
Curr Protoc Bioinformatics . 2007..Basic Protocol 2 discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. Basic Protocol 3 explains how to compare tree topologies using different tests...
- TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computingHeiko A Schmidt
Max Planck Institut fur Molekulare Genetik, Ihnestr 73, D 14195 Berlin, Germany
Bioinformatics 18:502-4. 2002..To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/)...
- pIQPNNI: parallel reconstruction of large maximum likelihood phylogeniesBui Quang Minh
Albert-Ludwigs-University Freiburg, Germany
Bioinformatics 21:3794-6. 2005..SUMMARY: IQPNNI is a program to infer maximum-likelihood phylogenetic trees from DNA or protein data with a large number of sequences. We present an improved and MPI-parallel implementation showing very good scaling and speed-up behavior...
- pIPHULA--parallel inference of population parameters using a likelihood approachHeiko A Schmidt
Center for Integrative Bioinformatics Vienna CIBIV, Max F Perutz Laboratories MFPL, Vienna, Austria
Bioinformatics 23:2636-7. 2007..pIPHULA is the parallel program to estimate the parameters of a realistic model of population growth...
- Genetic interaction between distinct Dobrava hantavirus subtypes in Apodemus agrarius and A. flavicollis in natureBoris Klempa
Institute of Virology, , Humboldt University, D-10098 Berlin, Germany
J Virol 77:804-9. 2003..DOBV-Af and DOBV-Aa are distinct but also subject to genetic exchanges that affect their evolutionary trajectories...
- Unexpected complexity of the Wnt gene family in a sea anemoneArne Kusserow
Institute of Zoology, Darmstadt University of Technology, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
Nature 433:156-60. 2005..It emphasizes the crucial function of Wnt genes in the diversification of eumetazoan body plans...
- An ancient Wnt-Dickkopf antagonism in HydraCorina Guder
Molecular Evolution and Genomics, Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
Development 133:901-11. 2006..Based on the corresponding expression patterns of hydkk1/2/4 and neuronal genes, we suggest that the body column of Hydra is a neurogenic environment suppressing Wnt signalling and facilitating neurogenesis...
- Rooted triple consensus and anomalous gene treesGregory B Ewing
Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, Dr, Bohr Gasse 9, A 1030 Vienna, Austria
BMC Evol Biol 8:118. 2008..In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs...