Control file for mlphase

Please see the examples in appendix A.5 and A.6. These control files show the two main modes of operation. The control file of the mlphase program contains:

a DATAFILE block: see the data file block section.

a MODEL block: see the model block section.

a FUNCTION block dependant on the operating mode of mlphase (see below)

Random seed: the seed for the random number generator.
Random seed = 13

Output file: the name of the file where the results are sent.
Output file = results/hiv-mlphase.output

The FUNCTION block contains specific parameters according to the mode of operation. At the moment, mlphase can ``Optimise user-defined phylogenetic trees'' or ``Search for ML topology''. When the user wants to optimise a set of defined trees the FUNCTION block contains the following fields:

Function: the parameter to specify the mode of operation.
Function = Optimise user-defined phylogenetic trees

Trees file: the name of the file containing the phylogenies, i.e., a set of trees in the Newick format with optional initial branch lengths values.
Trees file = primates.phylogenies

Number of trees: the user has to specify the number of trees in the previous file.
Number of trees = 4

Optimise model parameters: set this field to no if the model parameters are to be considered fixed, set it to yes if you want to optimise them.
Optimise model parameters = no

User's model parameters file: if the parameters are constant one must provide values for them. This field is for the name of the file containing the parameters for the model defined in the MODEL block. If provided when not required, the content of this file is used to initialise the parameters of the model before optimisation.
User's model parameters file = data/hiv-REV.model

When looking for the ML tree, the FUNCTION block contains:

Function: the parameter to specify the mode of operation.
Function = Search for ML topology

Topology search: this field specifies the search algorithm used to determine the phylogenies with the highest likelihood. At the moment the search algorithms implemented are Simple exhaustive search, Branch-and-bound exhaustive search and Heuristic stepwise addition.
Topology search = Heuristic stepwise addition

User defined monophyletic clades and Clade file: set the first field to yes if you want to constrain the search in the topology space. The second field is the name of your clade file.
User defined monophyletic clades = yes
Clade file = primates.clades

Optimise model parameters: set this field to no if the model parameters are to be considered fixed, set it to yes if you want to optimise them.
Optimise model parameters = yes

User's model parameters file: if the parameters are constant one must provide values for them, this field is for the name of the file containing the parameters for the model defined in the MODEL block.
User's model parameters file = data/primates-RNA7A.model