Density-functional thermochemistry. III. The role of exact exchange
Despite the remarkable thermochemical accuracy of Kohn–Sham density-functional theories with gradient corrections for exchange-correlation [see, for example, A. D. Becke, J. Che...
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359 publications
Fast and accurate short read alignment with Burrows–Wheeler transform
Abstract Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A...
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system...
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation o...
The MOS 36-item short-form health survey (SF-36). I. Conceptual framework and item selection.
A 36-item short-form (SF-36) was constructed to survey health status in the Medical Outcomes Study. The SF-36 was designed for use in clinical practice and research, health poli...
<i>OLEX2</i>: a complete structure solution, refinement and analysis program
New software, OLEX2 , has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-ori...
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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 thi...
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell gen...
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to fin...
HTSeq—a Python framework to work with high-throughput sequencing data
Abstract Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from stand...