It seems there is something wrong with TopologySearch.bf standard analysis. After I choose TopologySearch.bf under Phylogeny Reconstruction, select the data file (it always asks me for the data file even though I've opened the data file using File=>Open Data File and the data panel is there), select the standard models, I got the following error message:

A fatal error occured:
Failed to allocate - 4 bytes.
Current BL Command:treeStatistics =
{treesToBeSearched,1}
HYPHYKernel wil now quit
       Jh-oh!

Any idea about what happened?

Thanks,
luobin

Dear Luobin,

Standard analyses and GUI based analyses (e.g. data panels) etc, are disjoint (which is a bit counter-intuitive, but done so for historical reasons). Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for a package primer to see the difference between the two.

If you want to use topology inference using the GUI, follow along the lines of this example [http://www.hyphy.org/docs/GUIExamples/Example7.html] (modified for your specifics).

Alternatively, you can use the standard analyses without opening data panels and follow the prompts (including the one which loads the file).

HTH,
Sergei

Hi, Sergei,

Thanks for your explaination. I have one question when trying to run the analysis following the example by this link:

Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

The GUI does not have a model named MG94xHKY85_3x4, only MG94xHKY85_3x4_Rates is available. How can I get the model MG94xHKY85_3x4 into my GUI?

Thanks,
Luobin

Dear Luobin,

The MG94xHKY85_3x4 model has indeed gone missing. Download Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login and drop it inside SubstitutionModels/Codon to regain access to the model.

Cheers,
Sergei