PPT-Phylogeny - based on whole genome data

Johanne Ahrenfeldt PhD Student Overview What is Phylogeny How has it been used in the past Advantages of WGS based phylogeny Vibrio cholerae case BREAK How are we using it CSI phylogeny amp . Phylogenies. The process of evolution produces a pattern of relationships between species. . As . lineages evolve and split and modifications are inherited, their evolutionary paths diverge. . This . - based on whole genome data. Johanne Ahrenfeldt . Research Assistant. Overview. What is Phylogeny and what can it be used for. S. ingle . N. ucleotide . P. olymorphism (SNP) methods. - . snpTree. . Phylogeny. The evolutionary history of a species or group of species. . Convergent Evolution. A process in which species from different evolutionary branches may come to resemble each other if they live in similar environments and natural selection favored similar adaptions.. Systematics. Phylogeny. Phylon. = tribe, . geny. . = genesis or origin. The evolutionary history of a species or a group of related species.. Investigating the Tree of Life. Phylogeny: the evolutionary history of a species or group of species. http://galaxyproject.org/ for genome and epigenome analysis, and we illustrate how these two web services work together to identify epigenetic modifications that are charactephic (SNP-rich) promoters. Tandy Warnow. The University of Illinois at Urbana-Champaign. Brief history. We met in 1992, when I was working in the Discrete Algorithms Group at Sandia National Labs.. I moved to the University of Pennsylvania in 1993, then to the University of Texas at Austin in 1999. No papers yet. “Inferring Phylogenies” . Joseph Felsenstein. Excellent reference. What is a phylogeny?. Different Representations. Cladogram - branching pattern only. Phylogram - branch lengths are estimated and drawn proportional to the amount of change along the branch. CULTURE INDEPENDENT DIAGNOSTIC TESTING CIDTLook at the pathogens bacteria virus fungus under a microscopeBacteria often look alike even when stainedSometimes fairly specific Syphilis treponema Gram-ne Applications. Genome sequencing on the rise. Whole genome comparison provides a deeper understanding of biology. Evolutionary history. Non-coding regions. Variant detection. Methods. General two-fold approach. 1 Ascaris whole mtDNA 1 genomes 2 3 4 5 Peter Nejsum a ,b , * , 1 , Mohamed B. F. Hawash c , 1 , Martha Betson d , J. Russell Stothard e , Robin B. 6 Gasser f , Lee O. Andersen g 7 8 a Departme . Streptomycetaceae. Alan Ward. Motivation. Streptomyces . taxonomy. 16S. Whole genome sequencing. A bigger 16S phylogeny. Where is the diversity. The type strains. from NHGRI’s . Planning . Workshop on the Future Opportunities . for . Genome Sequencing . & Beyond. Mark Gerstein & Rick Myers. Recommendations related to genome function. . Part 1: Workshop summary (Mark). G-OnRamp Beta Users Workshop. Wilson Leung. 07/2016. Outline. Obtain genome assemblies from NCBI. Transfer . large genomics datasets to Galaxy. Common bioinformatics file formats . D. atatypes in Galaxy. October 20, 2011. From Carson Holt. Annotations. Automated. Ab. initio. (based on genomic sequence alone). Involves comparisons to known proteins (BLAST similarity). Sequence motifs such as start/stop .