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Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies

PARAMO pipline is a set of R scripts for reconstructing organismal ancestral anatomies. It appropriately models anatomical dependencies and uses ontology-informed amalgamation of stochastic maps to reconstruct phenotypic evolution at different levels of anatomical hierarchy including entire phenotypes. This approach provides new opportunities for tracking phenotypic radiations and evolution of organismal anatomies.

The PARAMO tutorial is given in PARAMO_pipeline.pdf, it can be viewed by clicking on the pdf file directly from within GitHub. To run the pipline, you need to copy it to your computer and follow the instructions given in the tutorail. To copy, use either "Cloned or download" icon in the right upper coner or the following command:

$ git clone git://