Sergei
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Hi Francesc,
[quote] This operator [code]:=[/code] makes the global parameters to be fixed, right? [/quote]
Yes, ':=' is the constraint assignment operator.
[quote]
I did a couple of changes in the script, Removing some comments and changing the model to make it easier to modify. So, if I want to use K2P with Kappa=2, the model will look like: [code] global AC := 1; global AT := 1; global AG := 2; /*I added AG now */ global CG := 1; global CT := 2; global GT := 1;
/* A C G T */ GTRRateMatrix = {{*, AC*t, AG*t, AT*t} {AC*t, *, CG*t, CT*t} {AG*t, CG*t, *, GT*t} {AT*t, CT*t, GT*t, * }}; [/code]
In the same way to have a HKY85 model, I would have to change the fixed frequencies for the estimated ones. [code] HarvestFrequencies (obsFreqs, myFilter, 1, 1, 1); [/code]
So, with this script any GTR model can be applied right?
[/quote]
Both of your examples are correct, and, indeed the GTR model can be applied by setting global model parameters (AC, AG etc) accordingly.
[quote] I will use this script for my pipeline with command-line hyphy. THe command line version of hyphy is not available in the dmg file for MAC OS X right? Do I have to compile it from source to get it? I am having some trouble to compile it in the Mac. [/quote]
Do you have Developer Tools installed on the Mac (it ships with the OS X disks, but is typically NOT installed by default)? Open a terminal and type in [code] g++ --version [/code]
at the prompt. If your gcc version is 4.2 or greater, then the standard Linux build instructions should generate a command line binary.
Sergei
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