Publications

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Abstract Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets...

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component...

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

This FAIRsharing record describes: SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archae...

An introduction to probability theory and its applications

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

MrBayes 3: Bayesian phylogenetic inference under mixed models

Abstract Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolution...

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, t...

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...