Darwin Help - Index

Created Oct 15, 2009 - 660 help topics.

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

A

AAAToInt	Alignment	AminoToInt	assign
AaFreqNoPat	AlignNucPepAll	antiparallel	assigned
abbreviation	AlignNucPepMatch	APC	AToCInt
abs	AlignOneAll	append	AToCodon
AC	AllIndices	ApproxSearchString	atoi
ActOut	AllQueryGrid	arcsin	AToInt
AddGrid	AllRootedTrees	arctan	avg
AddSpecies	AllTernaryRoots	AsciiToInt
Align	AltGenCode	assemble
AlignedSeq	aminoacids	assert

B

BackTranscribe	BBBToInt	BinTree	BrightenColor
BackTranslate	BestSearchString	BipartiteGraph	BToInt
BaseCount	Beta_Rand	Block
BaseToInt	Binomial_Rand	BootstrapTree

C

CalculateScore	Code	Complex	CreateCodonMatrices
CallExternal	CodonAlign	compress	CreateCProgram
CallSystem	CodonCode	CompressGrid	CreateDayMatrices
CaseSearchString	CodonCount	ComputeCAI	CreateDayMatrix
ceil	CodonDynProgStrings	ComputeCAIVector	CreateGrid
CenterTreeRoot	CodonMatrix	ComputeCubicTSP	CreateMSAMethods
ChangeLeafLabels	CodonMutate	ComputeDimensionlessFit	CreateOrigDayMatrix
CheckAmbigTree	CodonPamToPam	ComputeQuarticTSP	CreateRandMultAlign
ChiSquare_Rand	CodonToA	ComputeTPI	CreateRandPermutation
Cholesky	CodonToCInt	ComputeTSP	CreateRandSeq
CIntToA	CodonToInt	ConcatStrings	CreateString
CIntToAAA	CodonUsage	ConnectTcp	CreateSynMatrices
CIntToAmino	coeff	ConsistentGenome	CreateTreeConstruction
CIntToCodon	Collapse	conversion	CreateTreeConstructions
CIntToInt	CollapseNodes	convolve	CreateTreeStatistics
CircularTour	CollectStat	copy	Cumulative
Clique	Color	cor	CumulativeStd
CloseGrid	ColorPalette	cos	CurrentOff
Clustal	commandline	Counter
ClusterRelPam	Complement	Covariance
Clusters	ComplementSequence	CreateArray

D

darwin	Description	Domain	DrawTree
darwinipc	DigestAspN	DomainParameter	dSplitGraph
database	DigestionWeights	DownloadURL	dSplitIndex
DataMatrix	DigestSeq	dprint	dSplitMetricSum
date	DigestTrypsin	DrawDistribution	dSplits
DayMatrix	DigestWeights	DrawDotplot	DynProgGap
DayMatrixScale	disassemble	DrawGraph	DynProgMass
DBL_EPSILON	DisconMinimize	DrawHistogram	DynProgMassDb
DBL_MAX	DisconnectTcp	DrawPlot	DynProgNucPepString
DbToDarwin	DM	DrawPointDistribution	DynProgScore
debug	DMS	DrawSplitGraph	DynProgStrings
decompress	Document	DrawSplits
Denormalize	DoGapHeuristic	DrawStackedBar

E

Edge	enzymes	EstimatePam	ExpandFileName
EdgeComplement	EOF	EstimatePB93	ExpFit
Edges	erf	EstimateSynPAM	ExpFit2
Eigenvalues	erfc	eval	Exponential_Rand
EnterProfile	erfcinv	evalb	expx1
Entries	error	EvolTree	ExtendClass
Entry	EstimateCodonPAM	ExitProfile
enum	EstimateNG86	exp

F

factorial	FindCircularOrder	FindKey	FindSpeciesViolations
FDist_Rand	FindConnectedComponents	FindLongestRep	floor
FileStat	FindEntropy	FindNucPepPam	FlushGrid
FindBestScore	FindHighlyExpressedGenes	FindRules

G

Gamma	GetAaFrequency	GetNextGrid	GOdownload
GammaDist_Rand	GetAllNucPepMatches	GetOffset	GOname
Gap	GetComplement	GetPartitions	GOnumber
GapHeuristic	GetEntryInfo	GetPathDistance	GOsubclass
GapMatch	GetEntryNumber	GetPeptides	GOsubclassR
GapTree	GetFileInfo	getpid	GOsuperclass
GaussElim	GetGramRegionScore	GetPosition	GOsuperclassR
gc	GetGramSiteScore	GetSubTree_r	GramRegion
gcd	GetIntrons	GetTreeLabels	GramSchmidt
Gene	GetLcaSubtree	gigahertz	GramSite
GeneticCode	GetMachineUsage	GivensElim	Graph
GenomeSummary	GetMATreeNew	GlobalNucPepAlign	Graph_Rand
Geometric_Rand	GetMolWeight	Globals	GridFile
GetAaCount	GetMostFrequentGrams	GOdefinition

H

HammingSearchAllString	hastype	HTMLColor	HTMLRows
HammingSearchString	help	HTMLColorprint	HTMLTitle
has	History	HTMLCols	hydrophobicity
hash	hostname	HTMLprint

I

ID	Inherit	IntToAAA	ipcsend
IdenticalTrees	inputoutput	IntToAmino	iquo
Identity	Interior	IntToAscii	islower
If	InteriorTot	IntToB	IsolationIndex
ilogb	intersect	IntToBase	isupper
indets	IntOut	IntToBBB	iterate
InduceGraph	Intron	IntToCInt	iterator
Infix	IntronModel	IntToCodon
InfixNr	IntToA	invlogit

K

KWIndex

L

lasterror	libname	ln1x	log10
latex	LinearClassification	LnGamma	logit
lcoeff	LinearClassify	Lngamma	LongInteger
Leaf	LinearIntron	lnProbBallsBoxes	lowercase
LeastSquaresTree	LinearRegression	local	lprint
Leaves	List	LocalNucPepAlign	LSBestDelete
length	list	LocalNucPepAlignBestPam	LSBestSum
lg	ln	log	LSBestSumDelete

M

Machine	max	MinimizeBrent	mselect
MafftMSA	MaxCut	MinimizeFunc	MST
MAlign	MaxEdgeWeightClique	MinimizeSD	Multinomial_Rand
MAlignment	MaximizeFunc	MinSquareTree	MultipleSubTree
MapGrid	MaximizeRD	minus	Mutate
MapleFormula	MaxLikelihoodSize	MLTreeResult	MySql
Match	median	mod	MySqlResult
Matrices	member	MsaList
matrix	min	MSAMethod
matrix_inverse	Minimize2DFunc	MSAStatistics

N

names	noeval	NucDB	NucPepDynProg
naming	Normal_Rand	NucID	NucPepMatch
NBody	Normalize	nucleotides	NucPepRegions
Nodes	NSubGene	NucPepBackDynProg	NULL

O

objectorientation	OpenGrid	option	OutsideBounds
obsolete	OpenPipe	OptionalParameters
op	OpenReading	OrthologousGroup
OpenAppending	OpenWriting	Orthologues

P

PamMax	PASfromMSA	Postfix	ProbCloseMatches
PamToCodonPam	PASfromTree	PostscriptFigure	ProbDynProg
PamToPerIdent	PatEntry	PredictGenes	ProbIndex
PamWindows	Path	Prefix	ProbSeq
Paragraph	PepDB	Primes	procedure
ParallelAllNucPepMatches	PerIdentToPam	print	Process
ParExecuteIPC	Permutation	printf	product
ParExecuteTest	PhylogeneticTree	PrintIndex	profiling
parse	Pi	PrintInfo	Protect
ParseNewickTree	Plot2Gif	printlevel	Protein
ParsePred	PlotArguments	PrintMatrix	PruneTree
PartialFraction	PlotIndex	prints	PSDynProg
Partitions	Poisson_Rand	PrintStringMatch	PSubGene
Partitions_GetConflicts	Polar	PrintTreeSeq
Partitions_GetTree	PolishAngles	ProbAncestor
Partitions_ResolveConflicts	PositionTree	ProbBallsBoxes

Q

QueryGrid

R

Rand	ReadLine	ReconcileTree	Reverse
Rank	ReadOffsetLine	RedoCompletion	RGB_string
RAxML	ReadProgram	regexp	RobinsonFoulds
RBFS_Tree	ReadRawFile	Region	Roman
Readability	ReadRawLine	RegularGraph	Romberg
ReadBrk	ReadTable	RelativeAdaptiveness	RotateTree
ReadData	ReadTcp	remember	round
ReadDb	ReadURL	ReplaceString	RSCU
ReadDssp	ReceiveDataTcp	return	RunDarwinSession
ReadLibrary	ReceiveTcp	returntype

S

SaveEntries	SearchString	SignedSynteny	string
scalb	SearchTag	sin	string_RGB
ScaleIndex	selector	size	structures
ScoreAlignment	selectorfunction	sleep	Student_Rand
ScoreIntron	SendDataTcp	SmallAllAll	SubDist
ScoreNonSyn	SendTcp	sort	subs
ScoreSyn	seq	SortedMA	subset
SearchAC	sequal	SP_Species	SubTree
SearchAllArray	Sequence	SPCommonName	sum
SearchAllString	Sequences	Species_Entry	Surface
SearchArray	Set	SpeciesCode	SurfaceTot
SearchDayMatrix	set	SplitLines	SurfIntActPred
SearchDb	SetRand	sprintf	SurfOut
SearchDelim	SetRandSeed	SpToDarwin	SvdAnalysis
SearchFrag	SetupRA	sqrt	SvdBestBasis
SearchID	SetuptRNA	sscanf	SvdResult
SearchMassDb	ShortestPath	StatTest	symbol
SearchMultipleString	Shuffle	std	Synteny
SearchOrderedArray	sign	Std_Score	SystemCommand
SearchSeqDb	Signature	StoreKey

T

Table	TextHead	Translate	TreeSize
table	time	transpose	TreeStatistics
tan	TimedCallSystem	traperror	TreeToPam
TaxonId	TotalAlign	Tree	trunc
TempName	TotalTreeWeight	Tree_Graph	TT
TestStatResult	TPIDistr	TreeAngles	type
TetrahedronGraph	Transcribe	TreeConstruction	types

U

UnassignGlobals	UnionFind	UpdateStat
UncompressGrid	UnlabelLeaves	uppercase
union	UpdateSpeciesCode	UTCTime

V

var	VertexCover	ViewPlot
version	View	VisualizeProtein

W

Z

Zeta

zip

Zscore