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Assessing the root of bilaterian animals with scalable phylogenomic methods.
Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguñà J, Bailly X, Jondelius U, Wiens M, Müller WE, Seaver E, Wheeler WC, Martindale MQ, Giribet G, Dunn CW. Hejnol A, et al. Among authors: stamatakis a. Proc Biol Sci. 2009 Dec 22;276(1677):4261-70. doi: 10.1098/rspb.2009.0896. Epub 2009 Sep 16. Proc Biol Sci. 2009. PMID: 19759036 Free PMC article.
A functional phylogenomic view of the seed plants.
Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R. Lee EK, et al. Among authors: stamatakis a. PLoS Genet. 2011 Dec;7(12):e1002411. doi: 10.1371/journal.pgen.1002411. Epub 2011 Dec 15. PLoS Genet. 2011. PMID: 22194700 Free PMC article.
Phylogenomics resolves the timing and pattern of insect evolution.
Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspöck U, Aspöck H, Bartel D, Blanke A, Berger S, Böhm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schütte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TK, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X. Misof B, et al. Among authors: stamatakis a. Science. 2014 Nov 7;346(6210):763-7. doi: 10.1126/science.1257570. Epub 2014 Nov 6. Science. 2014. PMID: 25378627
The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.
Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, Collins GE, deWaard J, Dean J, Flint OS Jr, Hausmann A, Hendrich L, Hess M, Hogg ID, Kondratieff BC, Malicky H, Milton MA, Morinière J, Morse JC, Mwangi FN, Pauls SU, Gonzalez MR, Rinne A, Robinson JL, Salokannel J, Shackleton M, Smith B, Stamatakis A, StClair R, Thomas JA, Zamora-Muñoz C, Ziesmann T, Kjer KM. Zhou X, et al. Among authors: stamatakis a. Philos Trans R Soc Lond B Biol Sci. 2016 Sep 5;371(1702):20160025. doi: 10.1098/rstb.2016.0025. Philos Trans R Soc Lond B Biol Sci. 2016. PMID: 27481793 Free PMC article.
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 …
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
222 results