CAFE 4.2.1 significative expansions

[Emmanuelle Morin]

Hi,

I am using cafe 4.2.1 and I have generated results with a tree of 15 taxa and ~24,000 gene families.

I have done the different steps : filter out big families, lambda estimation, model error assessment.

My colleagues are wondering why some families are considered as significantly expanded and other not. Please find an example attached.

Can you give me an answer as why ?

Thanks,

Emmanuelle Morin

INRAE

[Dan Vanderpool]

Hello Emmanuelle,

It appears to me that you have a too distant outgroup.  Try deleting species 1 and re-running. 

Dan

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<CAFE_expanded_families.png>

__________________________

Dan Vanderpool
Postdoctoral Scholar
Department of Biology
Indiana University
Hahn Lab, Jordan Hall 249B
1001 East Third Street
Bloomington, IN 47405
Email: ddvand...@gmail.com