Control file for simulate

In appendix A.3 and A.4, example control files are provided for the first and the second mode of operation respectively.

The control file of the simulate program must provide

a MODEL block: see the model block section.

Retrieve the name of the model's parameters: a boolean field to specify the user's aim. Use yes for the first mode of usage mentionned above and no for the second mode.
Retrieve the name of the model's parameters = no

Model parameters file: if simulate is used to generate an example of a substitution model parameters file, the parameters are saved in a file having the name provided. When simulate is used to generate sequences, the user must provide parameters for the substitution model and they are read from the given file.
Model parameters file = simulate.model

The following fields may be required when simulate is used to generate sequences.

Random seed: the integer value provided with this field is used to initialise the random number generator.
Random seed = 1

Random tree and Tree file: simulate can either generate a random tree or use a supplied phylogeny. If Random tree is equal to yes then simulate generates a random tree and saves it in the specified file. If Random tree is equal to no then simulate parses the user tree from the specified file.
Random tree = no
Tree file = 8-species.tree

Number of species and Maximum branch length: when the Random tree field is set to yes, the user must provide the number of species and the maximum value for branch lengths in the generated the tree.
Number of species = 10
Maximum branch length = .4

Number of symbols from class i: you have to specify the number of symbols (e.g., number of nucleotides or number of paired sites) you want to generate for each class in your final sequence.
Number of symbols from class 1 = 100
Number of symbols from class 2 = 100
Number of symbols from class 3 = 100
Number of symbols from class 4 = 500
Number of symbols from class 5 = 300

Structure for the elements of class i: simulate can add a stucture in the generated data file in which case you have to specify the appropriate structure for the elements of each class.
Structure for the elements of class 1 = .
Structure for the elements of class 2 = .
Structure for the elements of class 3 = .
Structure for the elements of class 4 = .
Structure for the elements of class 5 = ()

Data file type and Total length of the raw sequences: simulate produces an input file following the format defined in the data file format section. To produce this file, you have to specify yourself the type and the length written in the first line. With the 5 classes described above:
Data file type = RNA
Total length of the raw sequences = 1400 #(100+100+100+500+300*2)

Output file: the name of the file where generated sequences are saved.
Output file = simulated-data/codons_and_rna.sequences