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. 2023 Feb 17;15(3):evad026. doi: 10.1093/gbe/evad026

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© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 2. — Phylogenetic tree for 40 gram‐positive bacteria. The phylogenetic tree includes two phyla (Actinobacteria and Firmicutes) and five classes (Actinobacteria, Bacilli, Clostridia, Coriobacteriia, and Tissierellia). An asterisk at the end of a class name indicates that the class is not monophyletic. (A) Species tree obtained using OrthoPhy with taxonomic information for five classes (branch lengths are in coalescent units, and all external branch lengths were set to 1; local posterior probability [Yin et al. 2019] is indicated in each internal branch). (B) Species tree obtained using OrthoPhy with taxonomic information for the two phyla (branch lengths in coalescent units, and all external branch lengths were set to 1; local posterior probability is indicated in each internal branch). (C) Species tree obtained using OF (local support values [Price et al. 2010] are indicated in each internal node). (D) Species tree obtained using OrthoFinder (support values are indicated in each internal node, summarizing the fraction of input trees that support its bipartition [Emms and Kelly 2019]). (E) Species tree obtained using OMA (branch lengths are in PAM units, and support values calculated by OMA are shown at each branch; Altenhoff et al. 2019).

Fig. 2. — Phylogenetic tree for 40 gram‐positive bacteria. The phylogenetic tree includes two phyla (Actinobacteria and Firmicutes) and five classes (Actinobacteria, Bacilli, Clostridia, Coriobacteriia, and Tissierellia). An asterisk at the end of a class name indicates that the class is not monophyletic. (A) Species tree obtained using OrthoPhy with taxonomic information for five classes (branch lengths are in coalescent units, and all external branch lengths were set to 1; local posterior probability [Yin et al. 2019] is indicated in each internal branch). (B) Species tree obtained using OrthoPhy with taxonomic information for the two phyla (branch lengths in coalescent units, and all external branch lengths were set to 1; local posterior probability is indicated in each internal branch). (C) Species tree obtained using OF (local support values [Price et al. 2010] are indicated in each internal node). (D) Species tree obtained using OrthoFinder (support values are indicated in each internal node, summarizing the fraction of input trees that support its bipartition [Emms and Kelly 2019]). (E) Species tree obtained using OMA (branch lengths are in PAM units, and support values calculated by OMA are shown at each branch; Altenhoff et al. 2019).