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saving analysis (Read 1915 times)
Gustavo Nolasco
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saving analysis
Mar 29th, 2006 at 10:12am
 
Hi,
I recently came up to Hyphy which appears a great software. However I could not yet discover how to save an analysis after the optimisation step - i.e, being able to recover the partition, LF and parameters table after re-opening HyPhy. On page 20 of the tutorial *.pdf file there is the sugestion to choose the option to include sequence saving and later opening the data as a batch file. However this is not working with me !
any clues?
Thanks, Gustavo
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Sergei
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Re: saving analysis
Reply #1 - Mar 29th, 2006 at 10:19am
 
Dear Gustavo,

There are two ways to go about saving an analysis:

1). If you set up the analysis using the GUI (i.e. based on the graphical data panel), then you can save the entire thing as suggested on page 20 of the tutorial: switch to the data panel you want to save, go to File->Save menu, and make sure to include the data in the file (there will be an pull-down menu in the file save dialog for that). You can later reopen the saved analysis by choosing File->Open Batch File and then selecting the previously saved analysis. Note, that you may have to reopen some of the windows (parameter table, trees etc) after you reload the analysis, because by default only the datapanel (with partitions) will be displayed.

2). If you want to export any kind of likelihood function (this is presently limited to functions based on a single alignment, albeit multiple partitions are also allowed), you can drop this file:

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into the UserAddIns directory of your HyPhy distribution, and then you will have access to the 'ExportLikelihoodFunction' option when you click on the button with two gears (top most on the bottom right) in the console window  (it's tool tip should say User Actions).

Cheers,
Sergei
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