Correction: Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups
Garance Sarton-Lohéac, Nikolai Romashchenko, Clément Marie Train, Sina Majidian, Natasha Glover
Abstract
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Taxonomy
TopicsLanguage and cultural evolution · Evolution and Genetic Dynamics · Evolutionary Game Theory and Cooperation
Correction to: Journal of Molecular Evolution (2025) 10.1007/s00239-025-10277-1
In Table 1 of this article, in the first column “Method (algorithm)” the below words were incorrectly written. For completeness and transparency, the old incorrect and the corrected versions of Table 1 are displayed below.
In Row 1, the word “OrthoL-oger” was incorrect and should have read “Ortho-Loger”
In Row 5, the word “Gen-eTrees” was incorrect and should have read “Gene-Trees”
In Row 6, the word “USE-ARCH” was incorrect and should have read “U-SEARCH”
In Addition to the above in Figure 8 legend, the word Orth-oXML was incorrect and should have read “Ortho-XML”.
Incorrect Table 1 Method (algorithm)Method typeSimilarity search methodClustering algorithmAlignment method (for tree building)Tree reconstruction methodReconciliation methodDatabase nameReferencesOrthoDB (OrthoL-oger)graph-basedMMSeqs2Triangulating and clustering all RBHs and in-paralogsN/AN/AN/AOrthoDB https://www.orthodb.org(Kriventseva et al. 2008, 2015; Kuznetsov et al. 2023; Tegenfeldt et al. 2024; Zdobnov et al. 2021)OMA (GETHOGs 2)graph-basedSmith-WatermanGETHOGS (identifies connected components + MinCut)N/AN/AN/AOmabrowser https://omabrowser.org(Altenhoff et al. 2013; Altenhoff et al. 2024a, b; Roth et al. 2008; C.-M. Train et al. 2017)PhylomeDB V5gene tree-basedBLASTseed gene + BLAST to other genomesMUSCLE, MAFFT, KALIGN, M-CoffeeMaximum likelihood IQ-TREE with different models. Best model selected with BICSpecies overlapPhylomeDB https://phylomedb.org(Fuentes et al. 2022; Huerta-Cepas et al. 2014)PANTHERgene tree-basedMapping sequences to curated families using HMMsTribe-MCLMAFFTGIGAGIGAPANTHER https://pantherdb.org(Mi et al. 2007, 2013; , 2017; Thomas 2010; Thomas et al. 2022)Ensembl-Compara (Gen-eTrees)gene tree-basedBLAST + Smith-Watermanhcluster_sg for phylogeny-aware clusteringM-Coffee or MAFFT for large groupsTreeBeSTTreeBeSTEnsemblCompara https://www.ensembl.org/info/genome/compara(Herrero et al. 2016; Vilella et al. 2009)Hieranoid 2hybridBLAST, USE-ARCH possibleInParanoidMUSCLENeighbor-Joining tree with BelvuETE3HieranoidDB https://hieranoidb.sbc.su.se(Kaduk & Sonnhammer 2017; Remm et al. 2001; Sonnhammer & Östlund 2015)OMA (FastOMA)hybridMapping sequences to HOGs with OMAmer; linclust for unmapped seqsGETHOGs 2MAFFTFastTreeSpecies overlapN/A(Majidian et al. 2025)eggNOG 6.0hybridMapping sequences COGs with eggNOG mapper; SIMAP on Smith-Waterman RBHs for unmapped seqs(COG) triangulating and clustering all RBHsMUSCLE, M-Coffee, Clustal Omega, MAFFTFastTree, PhyMLETE3eggNOG http://eggnog6.embl.de(Hernández-Plaza et al. 2023; Huerta-Cepas et al. 2016a, b; Powell et al. 2012, 2014)OrthoFinder 2.0hybridBLASTMCLMAFFTDendroBLAST + STAG + STRIDESpecies overlap + duplication-loss- coalescent modelN/A(Emms & Kelly 2015, 2019)MBGDhybridDIAMOND for pangenome construction; BLASTP + SW for top-level ortholog groupingDomClust + DomRefine (UPGMA domain-aware clustering)FAMSAFastTreeDomRefineMBGD https://mbgd.nibb.ac.jp(Uchiyama 2006; Uchiyama et al. 2025)
**Corrected Table ** 1 Method (algorithm)Method typeSimilarity search methodClustering algorithmAlignment method (for tree building)Tree reconstruction methodReconciliation methodDatabase nameReferencesOrthoDB (Ortho-Loger)graph-basedMMSeqs2Triangulating and clustering all RBHs and in-paralogsN/AN/AN/AOrthoDB https://www.orthodb.org(Kriventseva et al. 2008, 2015; Kuznetsov et al. 2023; Tegenfeldt et al. 2024; Zdobnov et al. 2021)OMA (GETHOGs 2)graph-basedSmith-WatermanGETHOGS (identifies connected components + MinCut)N/AN/AN/AOmabrowser https://omabrowser.org(Altenhoff et al. 2013; Altenhoff et al. 2024a, b; Roth et al. 2008; C.-M. Train et al. 2017)PhylomeDB V5gene tree-basedBLASTseed gene + BLAST to other genomesMUSCLE, MAFFT, KALIGN, M-CoffeeMaximum likelihood IQ-TREE with different models. Best model selected with BICSpecies overlapPhylomeDB https://phylomedb.org(Fuentes et al. 2022; Huerta-Cepas et al. 2014)PANTHERgene tree-basedMapping sequences to curated families using HMMsTribe-MCLMAFFTGIGAGIGAPANTHER https://pantherdb.org(Mi et al. 2007, 2013; , 2017; Thomas 2010; Thomas et al. 2022)Ensembl-Compara (Gene-Trees)gene tree-basedBLAST + Smith-Watermanhcluster_sg for phylogeny-aware clusteringM-Coffee or MAFFT for large groupsTreeBeSTTreeBeSTEnsemblCompara https://www.ensembl.org/info/genome/compara(Herrero et al. 2016; Vilella et al. 2009)Hieranoid 2hybridBLAST, U-SEARCH possibleInParanoidMUSCLENeighbor-Joining tree with BelvuETE3HieranoidDB https://hieranoidb.sbc.su.se(Kaduk & Sonnhammer 2017; Remm et al. 2001; Sonnhammer & Östlund 2015)OMA (FastOMA)hybridMapping sequences to HOGs with OMAmer; linclust for unmapped seqsGETHOGs 2MAFFTFastTreeSpecies overlapN/A(Majidian et al. 2025)eggNOG 6.0hybridMapping sequences COGs with eggNOG mapper; SIMAP on Smith-Waterman RBHs for unmapped seqs(COG) triangulating and clustering all RBHsMUSCLE, M-Coffee, Clustal Omega, MAFFTFastTree, PhyMLETE3eggNOG http://eggnog6.embl.de(Hernández-Plaza et al. 2023; Huerta-Cepas et al. 2016a, b; Powell et al. 2012, 2014)OrthoFinder 2.0hybridBLASTMCLMAFFTDendroBLAST + STAG + STRIDESpecies overlap + duplication-loss- coalescent modelN/A(Emms & Kelly 2015, 2019)MBGDhybridDIAMOND for pangenome construction; BLASTP + SW for top-level ortholog groupingDomClust + DomRefine (UPGMA domain-aware clustering)FAMSAFastTreeDomRefineMBGD https://mbgd.nibb.ac.jp(Uchiyama 2006; Uchiyama et al. 2025)
The original article has been corrected.