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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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, weExpand
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Mauve: multiple alignment of conserved genomic sequence with rearrangements.
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
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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homologyExpand
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PhyloSift: phylogenetic analysis of genomes and metagenomes
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
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BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
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 statisticalExpand
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Assemblathon 1: a competitive assessment of de novo short read assembly methods.
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 theExpand
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The Amphimedon queenslandica genome and the evolution of animal complexity
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 theExpand
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Reordering contigs of draft genomes using the Mauve Aligner
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 novelExpand
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An Integrated Pipeline for de Novo Assembly of Microbial Genomes
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 inExpand
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The design, implementation, and evaluation of mpiBLAST
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 ofExpand
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