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38 Publications visible to you, out of a total of 38
SPART: A versatile and standardized data exchange format for species partition information

Abstract

Not specified

Authors: Aurélien Miralles, Jacques Ducasse, Sophie Brouillet, Tomas Flouri, Tomochika Fujisawa, Paschalia Kapli, L. Lacey Knowles, Sangeeta Kumari, Alexandros Stamatakis, Jeet Sukumaran, Sarah Lutteropp, Miguel Vences, Nicolas Puillandre

Date Published: 2022

Publication Type: Journal

Empirical Numerical Properties of Maximum Likelihood Phylogenetic Inference

Abstract (Expand)

Phylogenetic trees represent hypothetical evolutionary relationships between organisms. Approaches for inferring phylogenetic trees include the Maximum Likelihood (ML) method. This method relies on … numerical optimization routines that use internal numerical thresholds. We analyze the influence of these thresholds on the likelihood scores and runtimes of tree inferences for the ML inference tools RAxML-NG, IQ-Tree, and FastTree. We analyze 22 empirical datasets and show that we can speed up the tree inference in RAxML-NG and IQ-Tree by changing the default values of two such numerical thresholds. Using 15 additional simulated datasets, we show that these changes do not affect the accuracy of the inferred phylogenetic trees. For RAxML-NG, increasing the likelihood thresholds lh_epsilon and spr_lh_epsilon to 10 and 103 respectively results in an average speedup of 1.9 ± 0.6. Increasing the likelihood threshold lh_epsilon in IQ-Tree results in an average speedup of 1.3 ± 0.4. In addition to the numerical analysis, we attempt to predict the difficulty of datasets, with the aim of preventing an unnecessarily large number of tree inferences for datasets that are easy to analyze. We present our prediction experiments and discuss why this task proved to be more challenging than anticipated.

Author: Julia Haag

Date Published: 31st Oct 2021

Publication Type: Master's Thesis

RAxML Grove: An empirical Phylogenetic Tree Database

Abstract

Not specified

Authors: Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis

Date Published: 6th Oct 2021

Publication Type: Journal

NetRAX: Accurate and Fast Maximum Likelihood Phylogenetic Network Inference ⋆

Abstract

Not specified

Authors: Sarah Lutteropp, Céline Scornavacca, Alexey M. Kozlov, Benoit Morel, Alexandros Stamatakis

Date Published: 31st Aug 2021

Publication Type: Journal

Swarm v3: towards tera-scale amplicon clustering

Abstract

Not specified

Authors: Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, Micah Dunthorn, Torbjørn Rognes

Date Published: 9th Jul 2021

Publication Type: Journal

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

Abstract

Not specified

Authors: Ben Bettisworth, Alexandros Stamatakis

Date Published: 25th Jun 2021

Publication Type: Journal

The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics

Abstract

Not specified

Authors: Nikolaos Psonis, Aglaia Antoniou, Emmanouela Karameta, Diego Darriba, Alexandros Stamatakis, Petros Lymberakis, Nikos Poulakakis

Date Published: 1st Jun 2021

Publication Type: Journal

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