old_contents:
global w;
global t;
global k;

LIKELIHOOD_FUNCTION_OUTPUT = 1;
RANDOM_STARTING_PERTURBATIONS = 1;

/* Include relevant functions */
#include "matrices.mdl"; //rate matrices
#include "GY94_Header.ibf";

/* Read in the data */
DataSet	raw_data = ReadDataFile("temp.fasta");

/* Filter the data to find and remove any stop codons*/
DataSetFilter   filt_data = CreateFilter(raw_data,3,"", "","TAA,TAG,TGA");

/* Collect observed frequencies into vectors */
HarvestFrequencies(observedFreq_data,filt_data,3,1,1);

/* Get the codon frequencies from the nucleotide frequency vectors */
codonFreq_data = BuildCodonFrequencies(observedFreq_data);

/* Define the model and tree */
Model MyModel = (GY94, codonFreq_data, 1);
UseModel (USE_NO_MODEL);
UseModel(MyModel);
Tree    Tree01 = DATAFILE_TREE;

/*COMPUTE LIKELIHOODS*/

LikelihoodFunction  LikFn2 = (filt_data, Tree01);

Optimize (paramValues2, LikFn2);
fprintf (stdout, LikFn2);

new_contents:
global w;
global t;
global k;

LIKELIHOOD_FUNCTION_OUTPUT = 1;
RANDOM_STARTING_PERTURBATIONS = 1;

/* Include relevant functions */
#include "matrices_fix_k.mdl"; //rate matrices
#include "GY94_Header.ibf";

/* Read in the data */
DataSet	raw_data = ReadDataFile("temp.fasta");

/* Filter the data to find and remove any stop codons*/
DataSetFilter   filt_data = CreateFilter(raw_data,3,"", "","TAA,TAG,TGA");

/* Collect observed frequencies into vectors */
HarvestFrequencies(observedFreq_data,filt_data,3,1,1);

/* Get the codon frequencies from the nucleotide frequency vectors */
codonFreq_data = BuildCodonFrequencies(observedFreq_data);

/* Define the model and tree */
Model MyModel = (GY94, codonFreq_data, 1);
UseModel (USE_NO_MODEL);
UseModel(MyModel);
Tree    Tree01 = DATAFILE_TREE;

/*COMPUTE LIKELIHOODS*/

LikelihoodFunction  LikFn2 = (filt_data, Tree01);

Optimize (paramValues2, LikFn2);
fprintf (stdout, LikFn2);

subject: Save the correct hyphy materials

message: Save the correct hyphy materials


subject: Add filling char to bf

message: Add filling char to bf