Olivier Gascuel

Sep 9, 2024 | medrxiv.org | Anna Zhukova |Olivier Gascuel

The authors have declared no competing interest. O.G. was supported by the Paris Artificial Intelligence Research Institute (PRAIRIE, ANR-19-P3IA-0001). I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Jun 28, 2024 | biorxiv.org | Frédéric Lemoine |Olivier Gascuel

AbstractFelsenstein's bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result in massive sampling of taxa (e.g. SARS-CoV-2). In this case, the sequences are very close, the trees are short, and the branches correspond to a small number of mutations (possibly 0). Nevertheless, these trees contain a strong signal, with unresolved parts but a low rate of false branches. With such data, Felsenstein's bootstrap is not satisfactory.

May 25, 2023 | mdpi.com | Anna Zhukova |David Dunn |Olivier Gascuel

2.5. Times of DRM LossTo estimate the DRM loss times, we used survival analysis with an exponential (constant hazard) model (Weibull model with β=1), implemented in Python3 package SurPyval (github.com/derrynknife/SurPyval accessed on 1 April 2023, v0.10.10). This model takes as input observations about event durations and estimates the rate at which the event occurs. The input data might be left-, right-, or interval-censored.