Performance assessment of phylogenetic inference tools using PhyloSmew.

ABSTRACT:

Motivation

The performance of phylogenetic inference tools is commonly evaluated using simulated as well as empirical sequence data alignments. An open question is how representative these alignments are with respect to those, commonly analyzed by users. Using the RAxMLGrove database, it is now possible to simulate DNA and amino acid 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 more realistic and representative simulated alignments.

Results

To automate this process, we implement PhyloSmew, a tool for benchmarking phylogenetic inference tools. We use it to simulate ∼20 000 multiple

SUBMITTER: Hohler D 

PROVIDER: S-EPMC12701799 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature