Kassian Kobert

Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo.

This paper introduces mPTP, an improved method for species delimitation that addresses limitations of PTP by incorporating intraspecific variation and using a faster algorithm, achieving better accuracy and scalability.

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.

Computing the Internode Certainty and related measures from partial gene trees.

The paper introduces methods to calculate internode and tree certainty from partial gene trees, showing that including partial trees affects results but full species trees are needed for meaningful measurements.

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.