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 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