Affiliation: Swiss Federal Institute of Technology
- Empirical codon substitution matrixAdrian Schneider
Institute of Computational Science, Swiss Federal Institute of Technology, Zurich, Switzerland
BMC Bioinformatics 6:134. 2005..Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution...
- Support patterns from different outgroups provide a strong phylogenetic signalAdrian Schneider
ETH Zurich, Department of Computer Science, Zurich, Switzerland
Mol Biol Evol 26:1259-72. 2009..It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla-Chiroptera clade...
- SynPAM-a distance measure based on synonymous codon substitutionsAdrian Schneider
ETH Zurich, Institute of Computational Science, Universitaetsstrasse, Zurich, Switzerland
IEEE/ACM Trans Comput Biol Bioinform 4:553-60. 2007..Comparisons with established measures of synonymous distance indicate that SynPAM has less variance and yields useful results over a longer time range...
- OMA Browser--exploring orthologous relations across 352 complete genomesAdrian Schneider
Institute of Computational Science, ETH Zurich, Switzerland
Bioinformatics 23:2180-2. 2007..Several large-scale efforts with various methodologies and scope tackle this problem, including OMA (the Orthologous MAtrix project)...
- A phylogenomic study of human, dog, and mouseGina Cannarozzi
Institute of Computational Science, ETH Zurich, Zurich, Switzerland
PLoS Comput Biol 3:e2. 2007....
- Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequencesChristophe Dessimoz
ETH Zurich, Institute of Computational Science, 8092 Zurich, Switzerland
BMC Bioinformatics 7:529. 2006..The most accurate method is currently maximum likelihood over the entire triplet. However, this approach is relatively time consuming...
- Improving phylogenetic inference with a semiempirical amino acid substitution modelStefan Zoller
Computational Biochemistry Research Group, ETH Zurich, Zurich, Switzerland
Mol Biol Evol 30:469-79. 2013....
- A new semiempirical codon substitution model based on principal component analysis of mammalian sequencesStefan Zoller
Department of Computer Science, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
Mol Biol Evol 29:271-7. 2012....
- OMA 2011: orthology inference among 1000 complete genomesAdrian M Altenhoff
ETH Zurich, Computer Science, Universitätstr 6, 8092 Zurich, Switzerland
Nucleic Acids Res 39:D289-94. 2011..In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org...
- Empirical analysis of the most relevant parameters of codon substitution modelsStefan Zoller
Computer Science Department, ETH Zurich, Zurich, Switzerland
J Mol Evol 70:605-12. 2010..For the third and subsequent PCs no simple descriptions could be found...