Lucas Czech

ybyra: Y-chromosome haplogroup calling using a tree-based scoring method

ybyra assigns Y-chromosome haplogroups using a tree-based scoring method and supports human and horse data.

Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana

This study observes rapid genetic adaptation and population dynamics in Arabidopsis thaliana across diverse climates over 5 years, showing predictable adaptation trends linked to survival and extinction risks.

Population and adaptation history of 739 Thlaspi arvense natural accessions

The paper analyzes 739 Thlaspi arvense accessions to uncover genetic variation and adaptation mechanisms, identifying genomic regions linked to agronomic traits and climate resilience.

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements

SCRAPP quantifies microbial sample diversity using phylogenetic placements and clustering, outperforming existing methods on empirical data.

Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data

The paper introduces GENESIS and GAPPA, tools for processing and analyzing phylogenetic data, offering efficiency and flexibility.

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples

The paper introduces scalable methods for analyzing and visualizing phylogenetic placements of metagenomic samples, showing they reveal new biological insights.

Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement

The paper introduces methods to automate reference phylogeny construction, enable large-scale phylogenetic placements on nested trees, and preprocess huge sequence datasets, improving speed and accuracy.

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

The paper introduces EPA-O_SCPLOWNGC_SCPLOW, a faster and more scalable phylogenetic placement algorithm for metagenomic data, outperforming existing methods by up to 30 times in sequential mode.