A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation

Open Access

Peer-reviewed

Research Article

Kalliopi Trachana ,

Contributed equally to this work with: Kalliopi Trachana, Kristoffer Forslund, Peer Bork

Affiliation Institute for Systems Biology, Seattle, WA, United States of America
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Kristoffer Forslund ,

Contributed equally to this work with: Kalliopi Trachana, Kristoffer Forslund, Peer Bork

Affiliation Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Tomas Larsson,

Affiliations Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany, Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Sean Powell,

Affiliation Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Tobias Doerks,

Affiliation Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Christian von Mering,

Affiliation Institute of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland
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Peer Bork

Contributed equally to this work with: Kalliopi Trachana, Kristoffer Forslund, Peer Bork

* E-mail: bork@embl.de

Affiliations Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany, Max-Delbruck-Centre for Molecular Medicine, Berlin, Germany
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Phylogenetic analysis
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Protein domains
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Phylogenetics
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Sequence alignment
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Horizontal gene transfer
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Bacterial genomics
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Species delimitation
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Evolutionary genetics
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