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High throughput phylogenomic analysis pipeline
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INSTALL
MANUAL
PhygOmics
README

README

PhyGomic

#########################
# * GENERAL DESCRIPTION #
#########################

 PhyGomic is a pipeline designed for the phylogenomic analysis of thousand of
sequences using two different approaches.

 + Phylogenetic Tree Topology Clustering Analysis (PTT analysis).
 
 + Omega (dN/dS ratio) or Genetic Selection Analysis (GS analysis).


#############################
# * PIPELINE REPRESENTATION #
#############################

        +------------------------------------+
        |                                    |
        |     Different Species/Strains      |
        |   Non Redundant Sequence Dataset   |
        |                                    |
        +------------------------------------+
                      ||
                      || CLUSTERING METHODS:
		      || + Too similar: Seq. assembly
		      || + Too different: Seq. homology searches
                      ||
                      \/
        +------------------------------------+
	|                                    |
        |          Sequence Clusters         |
        |   Homologous Gene Groups (HGG)     |
	|                                    |
	+------------------------------------+
                      ||
		      || ALIGN SEQUENCES
                      ||
		      \/
       +-------------------------------------+
       |                                     |
       |          Sequence Aligments         |
       |                                     |
       +-------------------------------------+
               ||                   ||
	       ||   PHYLOGENETIC    ||
	       ||     SOFTWARE      || 
               \/                   \/
       +----------------+   +----------------+
       |                |   |                |  		      
       |    Sequence    |   |    Sequence    |  
       | Clusters Trees |   | Clusters dN/dS |
       |                |   |                |
       +----------------+   +----------------+
               ||                   ||
               ||   PTT             ||    GS
               || Analysis          || Analysis
               \/                   \/
       +----------------+   +----------------+
       |                |   |                |
       |    Topology    |   |  dn/dS Values  |
       |    Clusters    |   |    Clusters    |
       |                |   |                |
       +----------------+   +----------------+ 


#############
# * VERSION #
#############

 Version 0.1: 11-2010
 Version 0.2: 08-2011

#############
# * AUTHORS #
#############

 Aureliano Bombarely
 (ab782@cornell.edu)
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