Tomáš Flouri

The impact of incomplete taxon sampling on inference of gene flow by Bayesian and summary methods using genomic sequence data

This study examines how incomplete taxon sampling affects gene flow inference using genomic data and introduces a Bayesian method to assess gene flow models.

Hierarchical heuristic species delimitation under the multispecies coalescent model with migration

The paper introduces a hierarchical heuristic method for species delimitation under the multispecies coalescent model, showing improved performance over existing methods in simulated and empirical data.

Inference of continuous gene flow between species under misspecified models

This study investigates biases in inferring gene flow between species under misspecified models and finds that pulse introgression models are more robust to model misspecification than continuous migration models.

SPART, a versatile and standardized data exchange format for species partition information

The paper introduces SPART, a standardized format for exchanging species partition information, to improve interoperability among species delimitation tools.

ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models

ModelTest-NG is a faster and more feature-rich tool for selecting DNA and protein evolutionary models, with improved accuracy and new functionalities.

RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference

RAxML-NG improves maximum likelihood phylogenetic inference with better accuracy, speed, and features like terrace detection and transfer bootstrap support.

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.

Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations

This paper introduces a method to identify and omit redundant operations in phylogenetic likelihood calculations, achieving significant speedup and memory reduction.

The divisible load balance problem with shared cost and its application to phylogenetic inference

The paper addresses load balancing in phylogenetic inference by modifying a data distribution algorithm to account for site repeats, achieving significant reductions in computational operations.

Two Independent and Highly Efficient Open Source TKF91 Implementations

The paper presents two open-source implementations of the TKF91 algorithm, developed by students as part of a programming course, showing identical results with minor numerical differences.

Are all global alignment algorithms and implementations correct?

The paper identifies two mathematical errors in Gotoh's global alignment algorithm, finds they are present in textbooks and implementations, and provides a corrected open-source implementation.