Changes between Version 20 and Version 21 of PhyloWS_workgroup

Timestamp:

2008/02/12 14:46:52 (17 years ago)

Author:

czmasek

Comment:

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PhyloWS_workgroup

@@ -15 +15 @@
 The Open Space discussion centered on the following issues:
  * The OTU (Operational Taxonomic Unit) perspective is an important use-case. 
-  * 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.
+  * 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.
   * 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.
   * 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).