Publications

fastp: an ultra-fast all-in-one FASTQ preprocessor

Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for e...

<i>PHENIX</i>: a comprehensive Python-based system for macromolecular structure solution

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to sol...

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

MRBAYES: Bayesian inference of phylogenetic trees

Abstract Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, doc...

Introduction to Quantitative Genetics.

Part 1 Genetic constitution of a population: Hardy-Weinberg equilibrium. Part 2 Changes in gene frequency: migration mutation. Part 3 Small populations - changes in gene frequen...

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...

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

BLAST+: architecture and applications

Abstract Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its ...

Search and clustering orders of magnitude faster than BLAST

Abstract Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. Results: UBLAS...

MODELTEST: testing the model of DNA substitution.

Abstract SUMMARY: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY: The MODELTEST package, includin...

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

The normalization strategy presented here is a prerequisite for accurate RT-PCR expression profiling, which, among other things, opens up the possibility of studying the biologi...

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasona...