Making friends with the software above, but some problems keep raising. First of all, I know that theoretically my MCMC construction should stop if I type the command stoppb , but it won't even let me type any more as soon as chain construction begins (my cmd goes completely deaf, even though the chain is being constructed). Secondly, how do I change the substitution model? If I wanted to use LG for example, what would the right command be? For me it only starts without errors if I type pb -d , but in this syntax the model is the one given default. How do I build in the model parameter? (in the manual it just gives you the models available but no examples on how to change this parameter are given)
First
Have you open a new terminal to stop the chain?
Second
To use a different model, you just add it to the [options] part of the command. For example, to use cat gtr models you would write a command like:
pb -d mydata.phylip -cat -gtr my.chain.name
Judith,
did you solve the problem for running phylobayes? I have the same problem, could you share the answer? Thank you.
Are you running Phylobayes in a Linux virtual machine from within Windows7, such as Cygwin? As mentioned above, you probably just need to open another terminal window or tab so you can run other commands or stop the Phylobayes run. Did you try typing Ctrl-C in the terminal window where it's running? That should terminate the process.
Were you able to change the model as I showed in my response above?
Thanks Cameron,
but this this is the first time I use this software. I installed Ubuntu on my laptop, and got the program Geany, It read the file Phylobayes.h, but then I do know what to do. I need an explanation for dummies.
If you know the way, please help me.
Daniel
Daniel: So to clarify, have you been able to open a terminal in Ubuntu and run phylobayes?
Daniel,
IU have actually switched to MrBayes meanwhile as I needed PhyloBayes only for the LG model. However, this has been implemented in the MrBayes as well to date, so I haven't really coped with PhyloBayes since then...
Hi Cameron,
I run PhyloBayes in the Ubuntu terminal and this is the result:
./PhyloBayes.h: line 1: class: command not found
./PhyloBayes.h: line 2: class: command not found
./PhyloBayes.h: line 3: class: command not found
./PhyloBayes.h: line 5: public: command not found
./PhyloBayes.h: line 8: //: Is a directory
./PhyloBayes.h: line 10: syntax error near unexpected token `MCParameters*'
./PhyloBayes.h: line 10: ` PhyloBayes(MCParameters* inParam);'
The Manual do not say what kind of info I should add. Just I am going to read and think to solve this.
Thanks for your reply,
I solved. Thank you for your answer. Of course I prefer use Mr.Bayes, but I need to use CAT.
"Detached" could be very useful to solve the problem of running multiple programs in the same time.
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