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Gene Phylogenies Analysis Web Interface: A Practical Guide

This walkthrough explores analyzing SOM of bipartitions from gene phylogenies. Understand the process of clustering gene families, visualizing multiple genomes, and reconstructing phylogenetic history. Learn about the advantages of using Self-Organizing Maps (SOMs) for gene clustering, without the need for pre-defined clusters, to visually represent commonalities and differences between clusters. Discover how to select clusters supporting specific bipartitions and explore gene families' evolutionary relationships. Ideal for researchers and students in molecular biology and bioinformatics.

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Gene Phylogenies Analysis Web Interface: A Practical Guide

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  1. A Web Interface to analyse SOM of Bipartitions of Gene Phylogenies - A Walk Through J. Peter Gogarten, Maria Poptsova Dept. of Molecular and Cell BiologyUniversity of Connecticut Neha Nahar, Lutz Hamel Department of Computer Science and Statistics University of Rhode Island

  2. BranchClust n Genomes Super Families Gene Families Reconstruct Phylogenetic History for Each Family

  3. Data Matrix Number of bipartitions (k) for N genomes is equal to 2(N-1)-N-1.

  4. Visualizing Multiple Genomes: SOMs • SOM  Self-Organizing Map • An artificial neural network approach to clustering • we are looking for clusters of genes which favor certain tree topologies • Advantages over other clustering approaches: • No a priori knowledge of how many clusters to expect • Explicit summary of commonalities and differences between clusters • Visually appealing representation T. Kohonen, Self-organizing maps, 3rd ed. Berlin ; New York: Springer, 2001.

  5. All clusters selected => ATV tree viewer applet (Zmasek & Eddy, Bioinformatics, 17, 383-384 2001) displays plurality consensus of all gene families. ATV allows to modify display

  6. Select branch to place root Select to re-root tree

  7. Euryarchaeota Root Cren-archaeota

  8. List of strongly supported bipartitions, including conflicts

  9. click to open map as pdf

  10. “well behaved” gene families select clusters that support bipartition

  11. gene families that group Archaeoglobus with Methanosarcina

  12. prolyl-tRNA synthetase, a gene family that groups the Halobacteria with the outgroup. This gene was acquired by the halobacterial lineage from the bacteria. These rare inter-domain gene transfers allow to correlate evolution in the three domains of life. (see Huang & Gogarten: Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends in Genetics 22 (7): 361-366. 2006)

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