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SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
SUPERSMART pipeline intro
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SUPERSMART pipeline intro

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Brief intro slides to the SUPERSMART workshop, 11-12 February 2013, by Karin Nilsson and Rutger Vos.

Brief intro slides to the SUPERSMART workshop, 11-12 February 2013, by Karin Nilsson and Rutger Vos.

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Transcript

  • 1. Self-Updating Platform for Estimating Rates of Speciationand Migration, Ages and Relationships of Taxa(SUPERSMART)Rutger Vos & Karin Nilsson
  • 2. GoalsTo develop an analysis workflow that: produces supermatrices of aligned sequences for a set of taxa of interest implements clever divide-and-conquer methods to build trees of any size from these supermatrices makes the resulting trees amenable to re-calibration using fossil anchors integrates the resulting chronograms into phylogeographical analyses makes these trees consumable by other phyloinformatic projects, such as OpenTOL, PhyloTastic and BioVeLSUPERSMART workshop, 11-12 February 2013 11 February 2013
  • 3. Usage scenarios• User wants a chronogram for an entire clade, e.g. Gentianales• User wants a chronogram for a selected list of species, e.g. all those within a geographical area• We want to assemble megatrees for integration downstream, e.g. to OpenTOLSUPERSMART workshop, 11-12 February 2013 11 February 2013
  • 4. Pipeline steps1. create a table of NCBI taxon IDs of interest2. write out and align the PhyLoTA clusters for these taxa3. since PhyLoTA clusters are limited by taxonomic breadth, somehow merge orthologous clusters (first: figure out whether they are orthologous)4. concatenate the merged clusters5. generate a starting tree6. run tree search SUPERSMART workshop, 11-12 February 2013 11 February 2013
  • 5. RDBMS architectureSUPERSMART workshop, 11-12 February 2013 11 February 2013
  • 6. Infrastructural needs• A unix-like environment, tested on MacOSX, various Linux flavours• MPI architecture (openMPI)• MySQL database• Standalone BLAST, exaML, phytime, muscle• Perl with dependenciesSUPERSMART workshop, 11-12 February 2013 11 February 2013
  • 7. Examples of preliminary results:Primates Strepsirrhines Tarsiers Apes Old world monkeys New world monkeys based on "all data" 11 February 2013SUPERSMART workshop, 11-12 February 2013
  • 8. Examples of preliminary results: Gentianales Gentianaceae Apocynaceae RubiaceaeLoganiaceae rbcL, ndhF, matK SUPERSMART workshop, 11-12 February 2013 11 February 2013
  • 9. To do / future work• Support for more types of sequences (so far: CDS, misc_RNA). For example: rRNA• Bootstrapping, i.e. write out bootstrapped versions of supermatrix, run independent searches on these, compute consensus• Recalibration based on fossils (e.g. treePL, r8s, BEAST)SUPERSMART workshop, 11-12 February 2013 11 February 2013
  • 10. Points of discussion Design Sustainability • Locus selection • Infrastructure • Taxonomic reconciliation • Funding • Orthology assignment • Developers • Divide and conquer • Collaborations (BioVeL, strategies OpenTOL, PhyloTastic) • Tool choice (aligners, Outreach tree-searchers, branch length scalers) • Website • Feature wish-list • Publications • Other use-cases • Workshops • CoursesSUPERSMART workshop, 11-12 February 2013 11 February 2013
  • 11. Thanks!

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