Ben Bettisworth

DGM Is Dead; Long Live DGM-Star! A Quantization-Theoretic Approach to Gamma Rate Discretization

The paper introduces a new method to discretize Gamma rate distributions in phylogenetics, reducing branch length bias compared to the standard DGM.

Quantifying and Predicting the Difficulty of Multiple Sequence Alignment with AlDiScore

The paper quantifies and predicts multiple sequence alignment difficulty using AlDiScore, achieving high R2 scores on unseen datasets.

bigrig: A range simulator for the DEC model

The paper introduces bigrig, a simulator for the DEC model of range evolution, validated with rigorous statistical testing and capable of generating data for large trees quickly.

raxtax: A k-mer-based non-Bayesian Taxonomic Classifier

raxtax is a fast, accurate k-mer-based taxonomic classifier that outperforms existing tools in speed while maintaining accuracy on large datasets.

Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads

This study evaluates how aDNA damage affects phylogenetic placement accuracy using empirical datasets and finds that read length dominates over other factors.

Lagrange-NG: The next generation of Lagrange

Lagrange-NG improves the efficiency and quality of ancestral range inference under the DEC model by introducing parallelization and better coding standards.

From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses

The paper introduces Pythia, a Random Forest Regressor that predicts the difficulty of phylogenetic analyses under the Maximum Likelihood model.

Phylourny: Predicting the Knock-out-phase of Tournaments via Phylogenetic Methods by example of the UEFA EURO 2020

The paper predicts the UEFA EURO 2020 knockout tournament outcomes using phylogenetic methods, finding France vs England as the most probable final with England having a slight edge.

RootDigger: a root placement program for phylogenetic trees

RootDigger computes the most likely root position on a phylogenetic tree using a non-reversible Markov model and provides confidence values for each possible root placement.

Empirical Analysis of Phylogenetic Quasi-Terraces

The paper analyzes the presence of quasi-terraces in phylogenetic tree space under linked and scaled partition models and shows their existence.