model TrNef

[andrezam...@yahoo.com.br]

Hi,

I run PF restricted to model available in MrBayes and I found that for one partition of my alignment I should use the TrNef + G model.

Is this model actually implemented in MrBayes?? How I set up in MrBayes?

Thanks.

[Rob Lanfear]

Hello,

The models that PartitionFinder assumes are in MrBayes are: "JC", "F81", "K80", "HKY", "SYM", "GTR"

That list doesn't include the TrNef model, so it looks like you might have set up your analysis wrong. Can you post your log.txt file and your .cfg file and I'll take a look.

Thanks,

Rob 

--
You received this message because you are subscribed to the Google Groups "PartitionFinder" group.
To unsubscribe from this group and stop receiving emails from it, send an email to partitionfind...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
Rob Lanfear
Research Fellow,
Ecology, Evolution, and Genetics,
Research School of Biology,
Australian National University

phone: +61 (0)2 6125 3611

www.robertlanfear.com

[Eliana Buenaventura]

Hi Rob, 

I also found TrNef+I+G model for one of my partitions when I run PF. I posted my log.txt file and .cfg files. I also would like to know how I set up in MrBayes?

Thanks, 

Eliana

[Rob Lanfear]

Hi Eliana,

MrBayes doesn't implement the TrNef model. 

Right now, you are running PartitionFinder with 'models=all;'. To  restrict it to only consider the models in MrBayes, you should change that to 'models=mrbayes;', then re-run your analysis. 

The analysis should run very fast, because all the results from the previous run will be saved. 

To find out how to define models in MrBayes, as long as they are implemented :), either take a look at the MrBayes Wiki for whatever version you use, or take a look at Brant Faircloth's excellent gist:

https://gist.github.com/brantfaircloth/895282

Let me know if you need any more help.

Cheers,

Rob

[Eliana Buenaventura]

Hi Rob, 

Thanks for your kind help and advice

The Brant Faircloth's gist was also very useful.

I have already set the models, and I got my results as fast as you said. 

Thanks again! :)

Eliana

--
You received this message because you are subscribed to a topic in the Google Groups "PartitionFinder" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/partitionfinder/1FshuTzSi9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to partitionfind...@googlegroups.com.

For more options, visit https://groups.google.com/groups/opt_out.
 
 

--

========================= 

Eliana Buenaventura

PhD Student

Department of Entomology

Natural History Museum of Denmark

University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, DENMARK

Tel: (57) 313 251 23 99

E-mail: elianabue...@gmail.com, eliana.bu...@snm.ku.dk

Home page: http://elianabuenaventura.webs.com

[andrezam...@yahoo.com.br]

Thanks Rob.

I was wrong. =]

[Rob Lanfear]

No worries! Better to post anyway. 

:)

On 3 July 2013 15:39, <andrezam...@yahoo.com.br> wrote:

Thanks Rob.

I was wrong. =]

--

You received this message because you are subscribed to the Google Groups "PartitionFinder" group.
To unsubscribe from this group and stop receiving emails from it, send an email to partitionfind...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.