Bo Xu has written a graphical user interface for BPP, called bppX. The compiled executables for windows, mac osx, and linux are available in the sourceforge file folder bppX. You install (unpack and compile) the current version of bpp first. Then unpack the GUI bppX. Then go to Function-Configuration to specify the folder name for the bpp files. Questions about bppX usage can be posted here.
Last edit: Rannala 2013-07-09
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Anonymous
Anonymous
-
2013-07-09
Ah, nevermind I got it!
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Anonymous
Anonymous
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2013-07-11
I am noticing that when I run the analysis it asks me "Species usedata?" Under the Utilities tab I selected 1: sqe like. I am attaching the bpp.ctl.tmp file...
It seems that you need add ; at the end of the tree. Otherwise the program bpp is still trying to read the tree and mistakes the next word in the control file (usedata) as a species name.
ziheng
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Anonymous
Anonymous
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2013-07-12
Great thanks. That solved that issue. However, while the sequences are loading bpp gets killed. No other error message is provided.
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Sorry for this very late reply. I think I missed the post earlier.
A problem is that bpp and the interface bppX communicate through files, and files have buffers, so the behavior of bpp may be different when it is run on the command line and when it is run from inside bppX. If you run bpp on the command line, you see every line of output immediately or so in windows at least. If you run bpp from inside bppX, the output is written in the file buffer and copied onto the screen only after the buffer is full. As a result you may not see all the screen output even if bpp has successfully read the sequences and has started the MCMC algorithm.
Anyway my suggestion is that you initially use small numbers for the MCMC section to run a very short chain, to check that the files are correct. Afterwards you change the variables to run a long chain.
Ziheng
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Anonymous
Anonymous
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2013-07-15
In the coast horned lizard example dataset ctl files, it appears that there are 8 values listed for the 7 finetune parameters. Is this a mistake?
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That is not a mistake or at least you don't need to worry.
The number of proposal steps depends on the model used.
Ziheng
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Anonymous
Anonymous
-
2014-08-16
Hi,
I tried to run bppX on my dataset, but the output file does not have posterior probabilities (only theta and tau values). I could open the tree in FigTree but without the posterior option. May you please help me in this regard? I used the following settings:
nSamples = 500000
samplefreq= 5
burnin= 50000
species delimitation= 0 (fixed species tree)
speciesmodel prior= 1: uniform rooted trees
Gtree = not selected (I also tried to run it with print Gtree. I got the following error: Could Not Find C:~\BPP\outfile'consense' is not recognized as an internal or external command)
Thanks.
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I've just installed bppX on my mac and noticed that the GUI interface is different than the one used in the youtube video by Bruce Rannala. Has the interfaced been updated or do I have an older version of bppx? If so, is the version used in Rannala's video still available?
Thanks
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Bo Xu has written a graphical user interface for BPP, called bppX. The compiled executables for windows, mac osx, and linux are available in the sourceforge file folder bppX. You install (unpack and compile) the current version of bpp first. Then unpack the GUI bppX. Then go to Function-Configuration to specify the folder name for the bpp files. Questions about bppX usage can be posted here.
Last edit: Rannala 2013-07-09
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I'm sorry. What is the "Function-Configuration"? I don't understand how to use the GUI.
Awesome. I just noticed that you cannot reduce the number of species under the Species and Tree tab.
i'll ask xu bo to check this.
ziheng
Ah, nevermind I got it!
I am noticing that when I run the analysis it asks me "Species usedata?" Under the Utilities tab I selected 1: sqe like. I am attaching the bpp.ctl.tmp file...
Chris
It seems that you need add ; at the end of the tree. Otherwise the program bpp is still trying to read the tree and mistakes the next word in the control file (usedata) as a species name.
ziheng
Great thanks. That solved that issue. However, while the sequences are loading bpp gets killed. No other error message is provided.
i am not sure. please try the examples in the bpp package first. you can open the control file from within the interface.
ziheng
The Chen example appears to work ok, but the lizard data set does not appear to load fully when run.
Apparently there is an issue with my data file(s). Can I send them to you to look over (via email)?
Sorry for this very late reply. I think I missed the post earlier.
A problem is that bpp and the interface bppX communicate through files, and files have buffers, so the behavior of bpp may be different when it is run on the command line and when it is run from inside bppX. If you run bpp on the command line, you see every line of output immediately or so in windows at least. If you run bpp from inside bppX, the output is written in the file buffer and copied onto the screen only after the buffer is full. As a result you may not see all the screen output even if bpp has successfully read the sequences and has started the MCMC algorithm.
Anyway my suggestion is that you initially use small numbers for the MCMC section to run a very short chain, to check that the files are correct. Afterwards you change the variables to run a long chain.
Ziheng
In the coast horned lizard example dataset ctl files, it appears that there are 8 values listed for the 7 finetune parameters. Is this a mistake?
That is not a mistake or at least you don't need to worry.
The number of proposal steps depends on the model used.
Ziheng
Hi,
I tried to run bppX on my dataset, but the output file does not have posterior probabilities (only theta and tau values). I could open the tree in FigTree but without the posterior option. May you please help me in this regard? I used the following settings:
nSamples = 500000
samplefreq= 5
burnin= 50000
species delimitation= 0 (fixed species tree)
speciesmodel prior= 1: uniform rooted trees
Gtree = not selected (I also tried to run it with print Gtree. I got the following error: Could Not Find C:~\BPP\outfile'consense' is not recognized as an internal or external command)
Thanks.
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HI,
I've just installed bppX on my mac and noticed that the GUI interface is different than the one used in the youtube video by Bruce Rannala. Has the interfaced been updated or do I have an older version of bppx? If so, is the version used in Rannala's video still available?
Thanks
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Is there a way to add more than 99 sequences per species in bppx?