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Aaron E. Darling
Researcher at University of Technology, Sydney
Publications - 146
Citations - 39014
Aaron E. Darling is an academic researcher from University of Technology, Sydney. The author has contributed to research in topics: Genome & Metagenomics. The author has an hindex of 45, co-authored 143 publications receiving 31849 citations. Previous affiliations of Aaron E. Darling include University of Queensland & University of California, Davis.
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Journal ArticleDOI
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space
Fredrik Ronquist,Maxim Teslenko,Paul van der Mark,Daniel L. Ayres,Aaron E. Darling,Sebastian Höhna,Bret Larget,Liang Liu,Marc A. Suchard,John P. Huelsenbeck +9 more
TL;DR: The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly, and provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates.
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Mauve: multiple alignment of conserved genomic sequence with rearrangements.
TL;DR: This work presents methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer and evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.
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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
TL;DR: A new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss is described, demonstrating high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental loss and loss.
Journal ArticleDOI
Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke,Patrick Schwientek,Alexander Sczyrba,Alexander Sczyrba,Natalia Ivanova,Iain Anderson,Jan Fang Cheng,Aaron E. Darling,Aaron E. Darling,Stephanie Malfatti,Brandon K. Swan,Esther A. Gies,Jeremy A. Dodsworth,Brian P. Hedlund,Georgios Tsiamis,Stefan M. Sievert,Wen Tso Liu,Jonathan A. Eisen,Steven J. Hallam,Nikos C. Kyrpides,Ramunas Stepanauskas,Edward M. Rubin,Philip Hugenholtz,Tanja Woyke +23 more
TL;DR: This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet.
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The Amphimedon queenslandica genome and the evolution of animal complexity
Mansi Srivastava,Oleg Simakov,Oleg Simakov,Jarrod Chapman,Bryony Fahey,Marie Gauthier,Marie Gauthier,Therese Mitros,Gemma S. Richards,Gemma S. Richards,Cecilia Conaco,Michael Dacre,Uffe Hellsten,Claire Larroux,Claire Larroux,Nicholas H. Putnam,Mario Stanke,Maja Adamska,Maja Adamska,Aaron E. Darling,Sandie M. Degnan,Todd H. Oakley,David C. Plachetzki,Yufeng Zhai,Marcin Adamski,Marcin Adamski,Andrew D Calcino,Scott F. Cummins,David Goodstein,Christina Harris,Daniel J. Jackson,Daniel J. Jackson,Sally P. Leys,Shengqiang Q. Shu,Ben J. Woodcroft,Michel Vervoort,Kenneth S. Kosik,Gerard Manning,Bernard M. Degnan,Daniel S. Rokhsar,Daniel S. Rokhsar +40 more
TL;DR: In this paper, the authors present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization.