Exercises 1. Hy-Phy automatically recognizes a variety of file formats, including NEXUS and PHYLIP variants. To see more clearly what this statement does, create and execute a simple batchfile with only the following code: DataSet myData = ReadDataFile ("../data/demo.seq"); fprintf(stdout,myData); 2. Create and execute a batchfile that uses the model of Jukes and Cantor (1969). The JC69 model differs from the F81 model only by imposing the assumption that all nucleotide frequencies are 0.25. 3. Users will often want to write batch files that are not aware of the name or location of the data file. One can ask Hy-Phy to prompt for a filename using the following syntax: SetDialogPrompt ("Please specify a nuleotide data or aminoacid file:"); DataSet myData = ReadDataFile (PROMPT_FOR_FILE); DataSetFilter filteredData = CreateFilter (myData,1); Modify basics.bf to prompt the user for the data file.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002