HYPHY Reference:
HYPHY Command Reference:
Command
Kind
Modified On
OPTIMIZE_SUMMATION_ORDER_PARTITION
Constant
9/5/2002
OPTIMIZE_SUMMATION_ORDER
Constant
9/5/2002
CreateFilter
Batch language command
9/3/2002
SimulateDataSet
Batch language command
8/22/2002
LIKELIHOOD_FUNCTION_OUTPUT
Constant
8/21/2002
TOKEN
Data File formatting instruction
8/20/2002
SCREEN_WIDTH
Constant
8/20/2002
SCREEN_HEIGHT
Constant
8/20/2002
RerootTree
Built-in function
8/20/2002
REPEAT
Data File formatting instruction
8/20/2002
ReadDataFile
Batch language command
8/20/2002
PRINT_DIGITS
Constant
8/20/2002
OPTIMIZATION_METHOD
Constant
8/20/2002
NICETY_LEVEL
Constant
8/20/2002
NEXUS_FILE_TREE_MATRIX
Constant
8/20/2002
MESSAGE_LOG
Constant
8/20/2002
LUSolve
Built-in function
8/20/2002
LUDecompose
Built-in function
8/20/2002
LF_CALL_COUNT
Constant
8/20/2002
IS_TREE_PRESENT_IN_DATA
Constant
8/20/2002
INTERMEDIATE_PRECISION
Constant
8/20/2002
GLOBAL_STARTING_POINT
Constant
8/20/2002
fscanf
Batch language command
8/20/2002
fprintf
Batch language command
8/20/2002
FORMAT
Data File formatting instruction
8/20/2002
ExecuteCommands
Batch language command
8/20/2002
END_OF_FILE
Constant
8/20/2002
Differentiate
Batch language command
8/20/2002
DATAFILE_TREE
Constant
8/20/2002
DATA_FILE_PRINT_FORMAT
Constant
8/20/2002
DATA_FILE_PARTITION_MATRIX
Constant
8/20/2002
COVARIANCE_PRECISION
Constant
8/20/2002
ConstructCategoryMatrix
Batch language command
8/20/2002
Bootstrap
Batch language command
8/20/2002
BASESET
Data File formatting instruction
8/20/2002
[]
Operation
8/20/2002
while
Batch language command
8/19/2002
UseModel
Batch language command
8/19/2002
Tree
Batch language command
8/19/2002
ReplicateConstraint
Batch language command
8/19/2002
ReconstructAncestors
Batch language command
8/19/2002
Permute
Batch language command
8/19/2002
Optimize
Batch language command
8/19/2002
OpenWindow
Batch language command
8/19/2002
OpenDataPanel
Batch language command
8/19/2002
MolecularClock
Batch language command
8/19/2002
Model
Batch language command
8/19/2002
LikelihoodFunction
Batch language command
8/19/2002
if..then..else
Batch language command
8/19/2002
HarvestFrequencies
Batch language command
8/19/2002
GetString
Batch language command
8/19/2002
GetInformation
Batch language command
8/19/2002
function
Batch language command
8/19/2002
for
Batch language command
8/19/2002
FindRoot
Batch language command
8/19/2002
do..while
Batch language command
8/19/2002
continue
Batch language command
8/19/2002
Category
Batch language command
8/19/2002
break
Batch language command
8/19/2002
=
Batch language command
8/19/2002
TEXTreeString
Built-in function
8/14/2002
PSTreeString
Built-in function
8/14/2002
ZCDF
Built-in function
8/9/2002
Rows
Built-in function
8/9/2002
<
Operation
8/9/2002
<=
Operation
8/9/2002
InvChi2
Built-in function
8/9/2002
>=
Operation
8/9/2002
>
Operation
8/9/2002
Abs
Built-in function
8/9/2002
ChoiceList
Batch language command
6/7/2001
CACHE_SUBTREES
Constant
6/7/2001
Min
Built-in function
6/6/2001
Max
Built-in function
6/6/2001
IBeta
Built-in function
6/6/2001
TipName
Built-in function
5/11/2000
Time
Built-in function
5/11/2000
SetParameter
Batch language command
5/11/2000
SelectTemplateModel
Batch language command
5/11/2000
Format
Built-in function
5/11/2000
DATA_FILE_DEFAULT_WIDTH
Constant
5/11/2000
Concatenate
Batch language command
5/11/2000
Combine
Batch language command
5/11/2000
CGammaDist
Built-in function
5/11/2000
CChi2
Built-in function
5/11/2000
CATEGORY_SIMULATION_METHOD
Constant
5/11/2000
BranchName
Built-in function
5/11/2000
BranchLength
Built-in function
5/11/2000
+
Operation
5/11/2000
-
Operation
5/11/2000
*
Operation
5/11/2000
/
Operation
5/11/2000
:=
Batch language command
5/11/2000
IGamma
Built-in function
5/10/2000
CovarianceMatrix
Batch language command
4/25/2000
MESSAGE_LOGGING
Constant
4/12/2000
TipCount
Built-in function
1/19/2000
OPTIMIZATION_PRECISION
Constant
1/19/2000
LAST_FILE_PATH
Constant
1/19/2000
CLEAR_FILE
Constant
1/19/2000
BranchCount
Built-in function
1/19/2000
ASSIGNED_SEED
Built-in function
1/19/2000
==
Operation
1/19/2000
!=
Operation
1/19/2000
USE_DISTANCES
Constant
8/17/1999
Transpose
Built-in function
8/17/1999
Tan
Built-in function
8/17/1999
Sqrt
Built-in function
8/17/1999
SKIP_OMISSIONS
Constant
8/17/1999
Sin
Built-in function
8/17/1999
SetDialogPrompt
Batch language command
8/17/1999
return
Batch language command
8/17/1999
RELATIVE_PRECISION
Constant
8/17/1999
RANDOM_STARTING_PERTURBATIONS
Constant
8/17/1999
RANDOM_SEED
Constant
8/17/1999
Random
Built-in function
8/17/1999
OPTIMIZATION_PRECSION_METHOD
Constant
8/17/1999
MAXIMUM_ITERATIONS_PER_VARIABLE
Constant
8/17/1999
Log
Built-in function
8/17/1999
LIST_ALL_VARIABLES
Constant
8/17/1999
KEEP_OPTIMAL_ORDER
Constant
8/17/1999
Inverse
Built-in function
8/17/1999
INTEGRATION_PRECISION_FACTOR
Constant
8/17/1999
#include
Batch language command
8/17/1999
GammaDist
Built-in function
8/17/1999
Gamma
Built-in function
8/17/1999
Exp
Built-in function
8/17/1999
Erf
Built-in function
8/17/1999
Cos
Built-in function
8/17/1999
Columns
Built-in function
8/17/1999
ClearConstraints
Batch language command
8/17/1999
BRACKETING_PERSISTENCE
Constant
8/17/1999
Beta
Built-in function
8/17/1999
Arctan
Built-in function
8/17/1999
ALLOW_BOUNDARY
Constant
8/17/1999
%
Operation
8/17/1999
$
Operation
8/17/1999
!
Operation
8/17/1999
&&
Operation
8/17/1999
||
Operation
8/17/1999
^
Operation
8/17/1999
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002