Darwin Help - Index

Created Jun 18, 2010 - 641 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	AlignedSeq	aminoacids	assemble
AaFreqNoPat	Alignment	AminoToInt	assert
abbreviation	AlignNucPepAll	antiparallel	assign
abs	AlignNucPepMatch	APC	assigned
AC	AlignOneAll	append	AToCInt
ActOut	AllIndices	ApproxSearchString	AToCodon
AddDeviation	AllRootedTrees	arcsin	atoi
AddSpecies	AllTernaryRoots	arctan	AToInt
Align	AltGenCode	AsciiToInt	avg

B

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

C

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

D

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

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	FindHighlyExpressedGenes	FindRules
FDist_Rand	FindConnectedComponents	FindLongestRep	FindSpeciesViolations
FileStat	FindEntropy	FindNucPepPam	floor

G

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

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

N

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

O

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

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

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	SearchTag	sin	string_RGB
scalb	selector	size	structures
ScaleIndex	selectorfunction	sleep	Student_Rand
ScaleTree	SendDataTcp	SmallAllAll	SubDist
ScoreAlignment	SendTcp	sort	subs
ScoreIntron	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	Stat	symbol
SearchMultipleString	Shuffle	StatTest	Synteny
SearchOrderedArray	sign	std	SystemCommand
SearchSeqDb	Signature	Std_Score
SearchString	SignedSynteny	string

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	UTCTime
union	UpdateSpeciesCode	uppercase

V

var	VertexCover	ViewPlot
version	View	VisualizeProtein

W

Z

Zeta

zip

Zscore