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 Biology University 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 Biapartiton #1 (** …. ….) … Biapartiton #k (*******..) Support value vector for a set #1 of orthologous genes P 11 … P 1k Support value vector for a set #2 of orthologous genes P 21 … P 2k … ……… Support value vector for a set #m of orthologous genes P n1 … P nk 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.

10. 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

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

12. Cren- archaeota Euryarchaeota Root

14. List of strongly supported bipartitions, including conflicts

15. click to open map as pdf

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

17. gene families that group Archaeoglobus with Methanosarcina

18. 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)