Affiliation: Stockholm University
- Bayesian gene/species tree reconciliation and orthology analysis using MCMCLars Arvestad
SBC and Center for Genomics and Bioinforamtics, Karolinska Instituet, SE 171 77, Stockholm, Sweden
Bioinformatics 19:i7-15. 2003..For orthology analysis, uncertainty has recently been addressed using parsimonious reconciliation combined with bootstrap techniques. However, until now no probabilistic methods have been available...
- primetv: a viewer for reconciled treesBengt Sennblad
Stockholm Bioinformatics Center and Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
BMC Bioinformatics 8:148. 2007..However, there exists a plethora of biologically relevant non-parsimonious reconciliations. Illustrations of these general reconciliations may not be achieved without manual editing...
- Genome-wide survey for biologically functional pseudogenesOrjan Svensson
Stockholm Bioinformatics Centre, Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
PLoS Comput Biol 2:e46. 2006..To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios...
- Efficient methods for estimating amino acid replacement ratesLars Arvestad
Stockholm Bioinformatics Center, AlbaNova University Center, Royal Institute of Technology KTH, SE 100 44, Stockholm, Sweden
J Mol Evol 62:663-73. 2006....
- GenPhyloData: realistic simulation of gene family evolutionJoel Sjöstrand
Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden
BMC Bioinformatics 14:209. 2013..The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock...
- DLRS: gene tree evolution in light of a species treeJoel Sjöstrand
Science for Life Laboratory, Stockholm University, SE 17121, Solna, Sweden
Bioinformatics 28:2994-5. 2012..PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters...
- Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstructionVolker Hollich
Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
Mol Biol Evol 22:2257-64. 2005..We also assessed the recently developed Scoredist measure, which performed equally well as more complex methods...
- The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genesSoraya Djerbi
Royal Institute of Technology, Department of Biotechnology, AlbaNova University Center, 10691, Stockholm, Sweden
Planta 221:739-46. 2005..The newly identified copies of CesA genes in P. trichocarpa give rise to a number of new questions concerning the mechanism of cellulose synthesis in trees...
- Evolution after gene duplication: models, mechanisms, sequences, systems, and organismsChristian Roth
Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
J Exp Zool B Mol Dev Evol 308:58-73. 2007..single gene duplication. Lastly, the role that these processes may have played in driving speciation is examined...