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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Gene Tree Construction and Correction Using SuperTree and Reconciliation.

Manuel Lafond, Cedric Chauve, Nadia El-Mabrouk

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |July 6, 2017
    PubMed
    Summary

    This study introduces a novel supertree framework for reconstructing gene trees from partial data. The developed algorithms efficiently correct gene trees, particularly improving weakly supported duplication nodes in phylogenetic analysis.

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    Area of Science:

    • Computational Biology
    • Phylogenetics
    • Bioinformatics

    Background:

    • Supertree methods are primarily used for species tree reconstruction.
    • Gene tree reconstruction from partial data presents unique challenges.
    • Existing methods may struggle with accurately representing gene duplication and speciation events.

    Purpose of the Study:

    • To adapt the supertree framework for gene tree reconstruction and correction.
    • To develop algorithms that minimize reconciliation cost for gene trees.
    • To preserve orthology and paralogy relationships during gene tree correction.

    Main Methods:

    • Developed a dynamic programming supertree algorithm for gene tree construction/correction.
    • Adapted the algorithm for gene trees with labeled nodes (duplication/speciation).
    • Created a quadratic time algorithm for correcting gene trees while preserving trusted subtrees and distances.

    Main Results:

    • The supertree framework effectively reconstructs gene trees from partial data.
    • Algorithms successfully correct gene trees, especially weakly supported duplication nodes.
    • Application to Ensembl gene trees demonstrates practical utility.

    Conclusions:

    • The supertree approach offers a powerful new framework for gene tree reconstruction and correction.
    • The developed algorithms provide efficient solutions for complex phylogenetic problems.
    • This work enhances the accuracy of gene tree inference, crucial for evolutionary studies.