Changes between Version 16 and Version 17 of PhyloWS_workgroup

Timestamp:

2008/02/12 14:07:36 (17 years ago)

Author:

czmasek

Comment:

--

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 the species tree. 
+  * 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 the species tree (i.e. measurement of the percentage of gene trees supporting an ecdysozoan versus a coelomata hypothesis).
   * Gene tree analysis: similar to the Zmasek et al (2007) paper, one may want to build alignments and phylogenetic trees for all ortholog families of a  gene family, or a pathway. After loading the trees into a database, one could then query the database for those gene trees that support a certain species phylogeny, for example the Ecdysozoan hypothesis.
    * Problem: the query topology will be given with either gene name labels, or species name labels, but the labels of the trees will be OTUs.