Substitution model selection in BEAST

105 views
Skip to first unread message

Ching Ching WEE

unread,
May 3, 2022, 2:17:36 PM5/3/22
to beast-users
Dear BEAST User

The best-fit model according to AICc using ModelFinder is : HIVw+F+I+G4

However, may I know which substitution model should I choose as both BEAST version did not have HIVw option as shown in the printscreen below?


2022-05-03 02_35_05-BEAUtiv.1.10.4.png

BEASTv.1.10.4


2022-05-03 02_35_47-BEAUti 2_ Standard.png

BEASTv2.6.7

In addition, how to specify 'F' (empirical frequencies)? I only see empirical frequencies option if the HKY substitution model is chosen (nucleotide). However, my data type is amino acids.


Remco Bouckaert

unread,
May 9, 2022, 8:51:20 PM5/9/22
to beast...@googlegroups.com
One way to achieve this in BEAST 2.6.7 is to install the OBAMA package (https://github.com/rbouckaert/obama/wiki/Installation), in the site model panel select the OBAMA model in the Site Model panel.

Instructions on using and interpreting the results of the OBAMA model are here: https://github.com/rbouckaert/obama/wiki/How-to-use-OBAMA

By default, it will average over the models selected that are checked in the list (see screenshot), but if you only have HIVw checked that is the only model that will be considered.

Remco




On 3/05/2022, at 11:43 AM, Ching Ching WEE <wching...@gmail.com> wrote:

Dear BEAST User

The best-fit model according to AICc using ModelFinder is : HIVw+F+I+G4

However, may I know which substitution model should I choose as both BEAST version did not have HIVw option as shown in the printscreen below?


<2022-05-03 02_35_05-BEAUtiv.1.10.4.png>

BEASTv.1.10.4


<2022-05-03 02_35_47-BEAUti 2_ Standard.png>

BEASTv2.6.7

In addition, how to specify 'F' (empirical frequencies)? I only see empirical frequencies option if the HKY substitution model is chosen (nucleotide). However, my data type is amino acids.



--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/4a737e73-ed09-4a13-aaa3-05e643d04d48n%40googlegroups.com.
<2022-05-03 02_35_05-BEAUtiv.1.10.4.png><2022-05-03 02_35_47-BEAUti 2_ Standard.png>

Reply all
Reply to author
Forward
0 new messages