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A representative Performance Assessment of Maximum Likelihood based Phylogenetic Inference Tools

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Abstract Summary The evaluation of phylogenetic inference tools is commonly conducted on simulated and empirical sequence data alignments. An open question is how representative these alignments are …tion is how representative these alignments are with respect to those, commonly analyzed by users. Based upon the RAxMLGrove database, it is now possible to simulate DNA sequences based on more than 70, 000 representative RAxML and RAxML-NG tree inferences on empirical datasets conducted on the RAxML web servers. This allows to assess the phylogenetic tree inference accuracy of various inference tools based on realistic and representative simulated DNA alignments. We simulated 20, 000 MSAs based on representative datasets (in terms of signal strength) from RAxMLGrove, and used 5, 000 datasets from the TreeBASE database, to assess the inference accuracy of FastTree2, IQ-TREE2, and RAxML-NG. We find that on quantifiably difficult-to-analyze MSAs all of the analysed tools perform poorly, such that the quicker FastTree2, can constitute a viable alternative to infer trees. We also find, that there are substantial differences between accuracy results on simulated and empirical data, despite the fact that a substantial effort was undertaken to simulate sequences under as realistic as possible settings. Contact Dimitri Höhler, dimitri.hoehler@h-its.org

Authors: Dimitri Höhler, Julia Haag, Alexey M. Kozlov, Alexandros Stamatakis

Date Published: 1st Nov 2022

Publication Type: Journal

ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms

Abstract

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Authors: Lukas Hubner, Demian Hespe, Peter Sanders, Alexandros Stamatakis

Date Published: 1st Nov 2022

Publication Type: Journal

The Free Lunch is not over yet – Systematic Exploration of Numerical Thresholds in Phylogenetic Inference

Abstract

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Authors: Julia Haag, Lukas Hübner, Alexey M. Kozlov, Alexandros Stamatakis

Date Published: 14th Jul 2022

Publication Type: Journal

From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses

Abstract

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Authors: Julia Haag, Dimitri Höhler, Ben Bettisworth, Alexandros Stamatakis

Date Published: 21st Jun 2022

Publication Type: Journal

Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade

Abstract

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Authors: Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera

Date Published: 26th May 2022

Publication Type: Journal

Lagrange-NG: The next generation of Lagrange

Abstract

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Authors: Ben Bettisworth, Stephen A. Smith, Alexandros Stamatakis

Date Published: 20th Apr 2022

Publication Type: Journal

SPART: A versatile and standardized data exchange format for species partition information

Abstract

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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

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