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- Publications
- Influence
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
- F. Ronquist, M. Teslenko, +7 authors J. Huelsenbeck
- Computer Science, Medicine
- Systematic biology
- 22 February 2012
Abstract Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we… Expand
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
- A. Darling, B. Mau, F. Blattner, N. Perna
- Biology, Medicine
- Genome research
- 1 July 2004
As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements,… Expand
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
- A. Darling, B. Mau, N. Perna
- Biology, Medicine
- PloS one
- 25 June 2010
Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology… Expand
PhyloSift: phylogenetic analysis of genomes and metagenomes
- A. Darling, Guillaume Jospin, E. Lowe, F. A. Matsen, H. Bik, J. Eisen
- Biology, Medicine
- PeerJ
- 9 January 2014
Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes.… Expand
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
- Daniel L. Ayres, A. Darling, +9 authors M. Suchard
- Medicine, Biology
- Systematic biology
- 1 October 2011
Abstract Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical… Expand
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
- D. Earl, Keith Bradnam, +68 authors B. Paten
- Medicine, Biology
- Genome research
- 16 September 2011
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the… Expand
The Amphimedon queenslandica genome and the evolution of animal complexity
- Mansi Srivastava, O. Simakov, +30 authors D. Rokhsar
- History, Medicine
- Nature
- 5 August 2010
Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the… Expand
Reordering contigs of draft genomes using the Mauve Aligner
- A. I. Rissman, B. Mau, B. Biehl, A. Darling, J. Glasner, N. Perna
- Computer Science, Medicine
- Bioinform.
- 10 June 2009
Summary: Mauve Contig Mover provides a new method for proposing the relative order of contigs that make up a draft genome based on comparison to a complete or draft reference genome. A novel… Expand
An Integrated Pipeline for de Novo Assembly of Microbial Genomes
- Andrew Tritt, J. Eisen, M. Facciotti, A. Darling
- Medicine, Biology
- PloS one
- 13 September 2012
Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in… Expand
The design, implementation, and evaluation of mpiBLAST
- A. Darling, L. Carey, Wu-chun Feng
- Computer Science
- 2003
mpiBLAST is an open-source parallelization of BLAST that achieves superlinear speed-up by segmenting a BLAST database and then having each node in a computational cluster search a unique portion of… Expand
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