about beast 2

[Lucas]

Could anyone tell me how to set GTR+gamma+invariant in beast 2?Thanks.

[Remco Bouckaert]

In BEAUti, import your alignment, then under the Site Model tab
- select GTR from the drop down box.
- set Gamma Category Count to 4.
- select estimate for shape -- assuming you want to estimate it from your data and do not already have an estimate.
- set Proportion Invariant to something larger than zero, say 0.1.
- select estimate for Proportion Invariant -- again, assuming you do not have an estimate for proportion invariant already.

Remco

________________________________________
From: beast...@googlegroups.com [beast...@googlegroups.com] on behalf of Lucas [mumuqi...@126.com]
Sent: Wednesday, 26 June 2013 11:25 p.m.
To: beast...@googlegroups.com
Subject: about beast 2

Could anyone tell me how to set GTR+gamma+invariant in beast 2?Thanks.

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[alicia alvarez]

Hello
I take this chain of old messages to ask something, really basic, related to the proportion of invariant sites.
I have estimated this proportion using jmodeltest. Is that ok if I indicate the value given by this software and do not check the "estimate" box?
Or it is advisable to put 0.1 and let beast to estimate the proportion?

Thanks,
Alicia