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Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees

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Bioinformatics Research and Applications (ISBRA 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10330))

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Abstract

Phylogenetic tree reconciliation is a widely used approach for analyzing the inconsistencies between the evolutionary histories of genes, and the species through which they have evolved. An important aspect of tree reconciliation are the cost functions involved that are the minimum number of evolutionary events explaining such inconsistencies. Mean values for these functions are fundamental when analyzing tree reconciliations. Here we describe mean value formulas when a history of genes is fixed for the cost functions for the events gene duplication, gene loss and gene duplication-loss, under the uniform model of species trees. We show that these formulas can be efficiently computed, and finally analyze the mean values using empirical and simulated data.

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Acknowledgements

This material is based upon work supported by the grants of the National Science Foundation under Grant No. 1617626 and the NCN #2015/19/B/ST6/00726.

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Authors and Affiliations

  1. Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland

    Paweł Górecki, Agnieszka Mykowiecka & Jarosław Paszek

  2. Department of Computer Science, Iowa State University, Ames, USA

    Alexey Markin & Oliver Eulenstein

Authors
  1. Paweł Górecki
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  2. Alexey Markin
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  3. Agnieszka Mykowiecka
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  4. Jarosław Paszek
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  5. Oliver Eulenstein
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Corresponding author

Correspondence to Paweł Górecki .

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Editors and Affiliations

  1. Georgia State University, Atlanta, Georgia, USA

    Zhipeng Cai

  2. University of Texas at Dallas, Richardson, Texas, USA

    Ovidiu Daescu

  3. Central South University, Changsha, China

    Min Li

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Górecki, P., Markin, A., Mykowiecka, A., Paszek, J., Eulenstein, O. (2017). Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees. In: Cai, Z., Daescu, O., Li, M. (eds) Bioinformatics Research and Applications. ISBRA 2017. Lecture Notes in Computer Science(), vol 10330. Springer, Cham. https://doi.org/10.1007/978-3-319-59575-7_21

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  • DOI: https://doi.org/10.1007/978-3-319-59575-7_21

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-59574-0

  • Online ISBN: 978-3-319-59575-7

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