Changes between Version 20 and Version 21 of PhyloWS_workgroup

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Timestamp:
2008/02/12 14:46:52 (11 years ago)
Author:
czmasek
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  • PhyloWS_workgroup

    v20 v21  
    1515The Open Space discussion centered on the following issues: 
    1616 * The OTU (Operational Taxonomic Unit) perspective is an important use-case.  
    17   * Gene tree analysis: splitting a given set of trees into subsets of trees as a function of compatibility to a given (set of) species tree(s). Degree of compatibility can be expressed as minimal sum of duplications needed to reconcile the gene with a species tree. I.e. measurement of the percentage of gene trees supporting an ecdysozoan versus a coelomata hypothesis. 
     17  * Species tree hypothesis testing: splitting a given set of trees into subsets of trees as a function of compatibility to a given (set of) species tree(s). Degree of compatibility can be expressed as minimal sum of duplications needed to reconcile the gene with a species tree. I.e. measurement of the percentage of gene trees supporting an ecdysozoan versus a coelomata hypothesis. 
    1818  * The analysis mentioned above could be extended by asking questions about the (majority of) functional categories supporting a given species tree. These examples require association of the following data with gene tree nodes: taxonomy identifier, gene identifier. 
    1919  * Gene tree analysis: similar to the Zmasek et al (2007) paper, one may want to build alignments and phylogenetic trees for all members of each protein  (family) of a biological network (e.g. apoptsis). After loading the trees into a database, one could then query the database for those gene trees that exhibit a given pattern (e.g. lineage specific gene expansion or gene loss).