Presence and absence relative to tree neighbors (instead of whole tree)

mattb112885 / clusterDbAnalysis

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes

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Presence and absence relative to tree neighbors (instead of whole tree) #34

Closed mattb112885 closed 10 years ago

mattb112885 commented 11 years ago

I should be able to wrap the existing presence/absence script to look for presence and absence in a clade relative only to neighboring clades (instead of relative to the entire tree) - this would make the analysis less sensitive to the choice of organisms to put in the tree and allow us to identify families that are gained or lost in multiple clades.

mattb112885 commented 10 years ago

We can now do this! See makeCoreClusterAnalysisTree --clades flag for details.