Navigation Banner
 
 HYPHY Command Reference:Batch Language Commands

Command Description Modified On
= Value assignment operator. Assigns the current value of the rhs to the lhs. To create dependancies use ':='. 8/19/2002
:= Dependance assignment operator. Assigns the formula defined by the rhs to the lhs. This operator should be used to constrain variables before optimization. 5/11/2000
Bootstrap Can be used to create samples with replacement of blocks of columns of 'unit' length of existing data sets or data set filters. 8/20/2002
break A loop termination command. When encountered within any for, while or do..while loop, causes the execution of the loop to stop, and transfers control to the first statement following the loop. 8/19/2002
Category Used to define a category (rate variation) variable. 8/19/2002
ChoiceList Used to present the user with a list of choices, and guides the user through the process of selecting one (or more) of them. If the user made a valid selection, then the string value of the selection is stored in the variable SELECTION_STRINGS. 6/7/2001
ClearConstraints Used to remove constraints on variables. 8/17/1999
Combine A command to merge several data sets into one. If the first argument is 'purge', then all the data sets used in the merge operation will be deleted after the operation is finished. The resulting data set contains all the data from the component data sets as stacked columns, i.e. column 1 is a vertical stack of all columns 1 from the component data sets. 5/11/2000
Concatenate A command to merge several data sets into one. If the first argument is 'purge', then all the data sets used in the merge operation will be deleted after the operation is finished. The resulting data set contains all the data from the component data sets as concatenated rows, i.e. row 1 is the concatenated rows 1 of all component data sets. 5/11/2000
ConstructCategoryMatrix Produces a matrix of category assignments for the sites of data analyzed with category variables. 8/20/2002
continue A loop 'forward'command. When encountered within any for, while or do..while loop, causes the rest of the commands within the loop to be ignored and forces execution back to the beginning of the loop. 8/19/2002
CovarianceMatrix CovarianceMatrix computes the approximate covariance matrix for the MLE of a given likelihood function. 4/25/2000
CreateFilter Used to select portions of data sets for inclusion in analyses. 'datasetid' is the identifier of the data set to filter. 'unit' is the size of the basic state for analyses in terms of the charchter length. 9/3/2002
Differentiate Find analytical derivative of an expression. Supports scalar expressions with +,-,*,/,^, Sin, Cos, Arctan, Log, Exp, Erf, Tan in them; correctly treats variable dependancies. Upon execution 'receptacle' will become a dependent variable, set equal to the derivative expression. 8/20/2002
do..while The 'do..while'loop. Cond is a logical expression. The loop is executed while Cond evaluates to non-zero. 8/19/2002
ExecuteCommands Interpret and execute a sequence of HyPhy batch language commands. 8/20/2002
FindRoot Find a root of an equation in a the interval [left_bound, right_bound]. Supports scalar expressions which HyPhy can differentiate. The equation solved is 'expression' = 0. Upon execution 'receptacle' is set to the root, or if no root could be found - to the value of left_bound. 8/19/2002
for The general 'for' loop construct. Very much like the C 'for'. Init consists of one statement (typically assignment). Cond is a logical statement (compound in general). Incr is the statement executed at the end of each loop iteration. 8/19/2002
fprintf Output command. Can be used to print essentially any object to a file or to stdout (console). 8/20/2002
fscanf Input command. Used to read values of numbers, matrices or trees from files or the console. 8/20/2002
function User defined function declaration. 8/19/2002
GetInformation GetString is a utility command returns a matrix whose contents vary upon the parameter value. 8/19/2002
GetString GetString is a utility command which returns a string, whose meaning varies, given some object. 8/19/2002
HarvestFrequencies This function allows one to collect the frequencies of characters (states) in a data set (or filter). 8/19/2002
if..then..else Flow control statement. 8/19/2002
#include File inclusion command. The file specified as the argument of the include command is inserted in place of the #include line. 8/17/1999
LikelihoodFunction The likelihood function construction operation. 8/19/2002
Model 'Model' is used to define an evolution model by specifying substitution rate matrix and equilibrium frequencies. 8/19/2002
MolecularClock Molecular clock is called to set additive length constraints on a tree from a node down. 8/19/2002
OpenDataPanel This function is used to save and restore states of data panel windows in HyPhy GUI. It is not recommended for direct invokation by the user. 8/19/2002
OpenWindow This command opens windows of HyPhy GUI from batch language files. 8/19/2002
Optimize 'Optimize' performs the optimization of the likelihood function. 8/19/2002
Permute Can be used to create permutations of blocks of columns of 'unit' length of existing data sets or data set filters. 8/19/2002
ReadDataFile Data file reading instruction. 8/20/2002
ReconstructAncestors Reconstructs the list of ancestral sequences based on current parameter values. The sequences are reconstructed by finding the states of internal tree nodes which maximize the likelihood of the tree. 8/19/2002
ReplicateConstraint ReplicateConstraint exists to facilitate defining tree (or subtree) wide constraints. It allows to replicate a single constraint throughout the matching parts of a tree or several trees. 8/19/2002
return The 'return' statement for user functions. 8/17/1999
SelectTemplateModel Prompts the user to select a template model appropriate for the data contained in 'filterid'. 5/11/2000
SetDialogPrompt Used to set the prompt string presented to the user when PROMPT_FOR_STRING or PROMPT_FOR_FILE is used. 8/17/1999
SetParameter SetParameter is used to assign a value to independent parameters of the likelihood function. 5/11/2000
SimulateDataSet Data file simulation instruction. 8/22/2002
Tree Tree construction command. 8/19/2002
UseModel Used to select a model to be attached to branches of trees subsequently. 8/19/2002
while The 'while'loop. 8/19/2002

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002