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Quantifying the phylodynamic forces driving papillomavirus evolution.
Gottschling M, Göker M, Stamatakis A, Bininda-Emonds OR, Nindl I, Bravo IG. Gottschling M, et al. Among authors: stamatakis a. Mol Biol Evol. 2011 Jul;28(7):2101-13. doi: 10.1093/molbev/msr030. Epub 2011 Jan 31. Mol Biol Evol. 2011. PMID: 21285031
Aligning short reads to reference alignments and trees.
Berger SA, Stamatakis A. Berger SA, et al. Among authors: stamatakis a. Bioinformatics. 2011 Aug 1;27(15):2068-75. doi: 10.1093/bioinformatics/btr320. Epub 2011 Jun 2. Bioinformatics. 2011. PMID: 21636595
RAxML-Light: a tool for computing terabyte phylogenies.
Stamatakis A, Aberer AJ, Goll C, Smith SA, Berger SA, Izquierdo-Carrasco F. Stamatakis A, et al. Bioinformatics. 2012 Aug 1;28(15):2064-6. doi: 10.1093/bioinformatics/bts309. Epub 2012 May 24. Bioinformatics. 2012. PMID: 22628519 Free PMC article.
To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20 000 000 bp) using 672 cores. This dataset requires one terabyte of RAM to compute the likelihood score on a single tree. CODE AVAILABILI …
To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20 000 …
Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. Sunagawa S, et al. Among authors: stamatakis a. Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20. Nat Methods. 2013. PMID: 24141494
221 results