Local and relaxed clocks: the best of both worlds by Mathieu Fourment, Aaron E. Darling

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Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics by Mathieu Fourment, Aaron E. Darling

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A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq by Catherine M. Burke, Aaron E. Darling

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Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C) by Matthew Z. DeMaere, Aaron E. Darling

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progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. by Aaron E Darling, Bob Mau, Nicole T Perna

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bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes by Matthew Z. DeMaere, Aaron E. Darling

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qc3C: Reference-free quality control for Hi-C sequencing data. by Matthew Z DeMaere, Aaron E Darling

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The impact of migratory flyways on the spread of avian influenza virus in North America by Mathieu Fourment, Aaron E. Darling, Edward C. Holmes

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Dynamics of genome rearrangement in bacterial populations. by Aaron E Darling, István Miklós, Mark A Ragan

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Strainberry: automated strain separation in low-complexity metagenomes using long reads by Riccardo Vicedomini, Christopher Quince, Aaron E. Darling, Rayan Chikhi

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An integrated pipeline for de novo assembly of microbial genomes. by Andrew Tritt, Jonathan A Eisen, Marc T Facciotti, Aaron E Darling

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Are protein domains modules of lateral genetic transfer? by Cheong Xin Chan, Aaron E Darling, Robert G Beiko, Mark A Ragan

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Rhometa: Population recombination rate estimation from metagenomic read datasets. by Sidaswar Krishnan, Matthew Z DeMaere, Dominik Beck, Martin Ostrowski, Justin R Seymour, Aaron E Darling

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DESMAN: a new tool for de novo extraction of strains from metagenomes by Christopher Quince, Tom O. Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E. Darling, Gavin Collins, A. Murat Eren

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Swabs to genomes: a comprehensive workflow by Madison I. Dunitz, Jenna M. Lang, Guillaume Jospin, Aaron E. Darling, Jonathan A. Eisen, David A. Coil

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PhyloSift: phylogenetic analysis of genomes and metagenomes by Aaron E. Darling, Guillaume Jospin, Eric Lowe, Frederick A. Matsen IV, Holly M. Bik, Jonathan A. Eisen

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Whole Genome Sequencing Analysis of Porcine Faecal Commensal <i>Escherichia coli</i> Carrying Class 1 Integrons from Sows and Their Offspring by Tiziana Zingali, Cameron J. Reid, Toni A. Chapman, Daniela Gaio, Michael Liu, Aaron E. Darling, Steven P. Djordjevic

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Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes by Daniel R. Bogema, Melinda L. Micallef, Michael Liu, Matthew P. Padula, Steven P. Djordjevic, Aaron E. Darling, Cheryl Jenkins

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Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products by Christopher W. Beitel, Lutz Froenicke, Jenna M. Lang, Ian F. Korf, Richard W. Michelmore, Jonathan A. Eisen, Aaron E. Darling

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Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig. by Daniela Gaio, Matthew Z DeMaere, Kay Anantanawat, Graeme J Eamens, Linda Falconer, Toni A Chapman, Steven Djordjevic, Aaron E Darling

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