An investigation of irreproducibility in maximum likelihood phylogenetic inference.
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ABSTRACT:
SUBMITTER: Shen XX
PROVIDER: S-EPMC7705714 | biostudies-literature | 2020 Nov
REPOSITORIES: biostudies-literature
Publications
An investigation of irreproducibility in maximum likelihood phylogenetic inference.
Shen Xing-Xing XX Li Yuanning Y Hittinger Chris Todd CT Chen Xue-Xin XX Rokas Antonis A
Nature communications 20201130 1
Phylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515 (18.11%) IQ-TREE-inferred and 1813 (9.34%) RAxML-NG-inferred maximum likelihood (ML) gene trees are topologically irreproducible when executing two replicates (Run1 and Run2) for each of 19,414 gene alignments in 15 animal, plant, and fungal phylogenomic datasets. Notably, coalescent-based ASTRAL species phylogenies inferred from Run1 and ...[more]
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