treebase and phyloinformatics roderic page university of glasgow
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TreeBASE and Phyloinformatics
Roderic PageUniversity of Glasgow
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At the core of a ToL effort must be a “phyloinformatic intrastructure”
Tools for:
• data and tree storage
• analysis (supertrees, supermatrices)
• collaboration
• meta analysis
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It’s a scandal
• We cannot answer even the most basic question: “what is the phylogeny for group x?”
• GenBank is currently the best phylogenetic database(!)
• Can't even say how many species are in a given group
• Little idea of who is doing what
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Tree of Lifetolweb.org
• Provides text and images
• Relies on extensive manual effort (e.g., writing text)
• Can’t do any computations with it
• Limited research value
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TreeBASEwww.treebase.org
• Relational database
• Query by author, taxon, study number
• Compute supertrees
• Submit NEXUS data files
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TreeBASE and mincut supertrees
• User selects two or more trees
• Clicks on button
and script on darwin.zoology.gla.ac.uk is run to create supertree
• Can view as PS, PDF, treefile, or in Java applet (ATV)
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Dependencies amongst studies (Gatesy et al.)
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What’s wrong with TreeBASE?
• No consistency of taxon names
• (e.g., Human, Homo sapiens, Homo sapiens X54666-1)
• No consistency of data names (e.g., gene names, morphological characters, etc.)
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What needs to be done to TreeBASE?
• Consistency of taxon names
• Consistency of data names (e.g., gene names)
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General issues• Develop tools for rapid construction of supertrees and
supermatrices
• Visualisation of trees (and other graphs)
• Queries to highlight areas of uncertainty
• Easy submission of rigorously annotated data
• Resolve centralisation versus distributed (one database or many?)
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The single most important thing we could do is to create a
phyloloinformatic infrastructure
to support ToL studies
(IMHO)
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Primary Database
Comparative DataPhylogenetic Trees
Higher TaxonName Database
Synthetic Viewof
Tree of Life
Synthetic Viewof
Tree of Life....additionalsyntheses
Secondary Databases
PII
SequenceDatabases
Species NameDatabases
Collections andVoucher Specimen
Databases
BiologicalDatabases
BiologicalDatabases
Phylogenetically drivenqueries
.....