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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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.
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
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.
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
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.
Insights into the phylogeny and coding potential of microbial dark matter
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.
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference, is presented, which provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms.
PhyloSift: phylogenetic analysis of genomes and metagenomes
- A. Darling, G. Jospin, E. Lowe, Frederick Albert Matsen IV, H. Bik, J. Eisen
- 9 January 2014
This work presents an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample and applies new tools to analyze the phylogenetic diversity of microbial communities.
The Amphimedon queenslandica genome and the evolution of animal complexity
Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes.
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
The Assemblathon 1 competition is described, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies, and it is established that it is possible to assemble the genome to a high level of coverage and accuracy.
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains, and parameter settings markedly affected performance, underscoring their importance for program reproducibility.
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming, resulting in substantially improved assemblies that recover a more complete set of reference genes than previous methods.