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caitiecollins / treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
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about the recombination #30

Closed zhaoxvwahaha closed 5 years ago

zhaoxvwahaha commented 5 years ago

Hi,

If my tree doesn't be constructed by recombination-aware approach, can treeWAS still consider this confounding effect in analysis.

Thanks in advance for your reply.

xavierdidelot commented 5 years ago

Yes you can use a standard phylogenetic tree, and treeWAS will still use the distribution of homoplasies against this tree to build up a picture of how much recombination should be corrected for. But we still recommend that treeWAS should be used alongside ClonalFrameML as described here https://github.com/caitiecollins/treeWAS/wiki/4.-Interpreting-Output