software
My programming language of choice is C++, with some work in Python, Snakemake, and others. I am aiming at software design that is clean and free of clutter. With the ongoing growth of biological data, a major focus of my research is the development of high-performance genomics tools.
grenedalf
A command line tool for population genetic analysis of pool-sequencing data, which is more convenient to use, and several orders of magnitude faster than competitors. It offers highly customizable commands for typical population genetic statistics, such as FST and Tajima's D.
grenepipe
A workflow for variant calling and pool-sequencing frequency calling from raw sequences, which automates the full pipeline: read trimming, mapping and calling, with configurable tools in each step. It has been used extensively in large-scale projects such as GrENE-net.
gappa
A command line tool for analyzing and visualizing phylogenetic placement data. It implements the methods described in the here and here section, has a simple interface with lots of options for most use cases, and is orders of magnitude faster than previous tools. See also here for my review on phylogenetic placement.
genesis
My main C++ library for phylogenetic and population genetic file formats, algorithms, analyses, and visualizations, developed for my research projects and publications. As it can be used at both the production stage (conducting data analyses) as well as the development stage (rapid prototyping), it has proven useful in many projects. It is the best scoring code in a comprehensive software quality evaluation of bioinformatics tools, see here.