Darwin v.1.6 to v.2.0 Commands old.scr AAAP AAAToInt old.scr ACS AC old.scr AP AToInt old.scr AaCount GetAaCount old.scr AaFrequency GetAaFrequency old.scr AddGF AddGrid old.scr AlignGaps AdjustGaps old.scr AlignedIntrons GetIntrons old.scr AlignedPeptide GetPeptides old.scr AllMatches GetAllMatches old.scr AminoP AminoToInt old.scr ApprTextSearch ApproxSearchString old.scr BBBC NucToCode old.scr BBBP NucToInt old.scr BP NToInt old.scr BBBP NuctoInt old.scr BackDynProgr BackDynProg old.scr BaseP NucleicToInt old.scr BestPamMatch GetPam old.scr BestPamShake LocalAlignBestPam old.scr BestStringMatch SearchString old.scr BisectTree DrawBisectTree old.scr CBBB CodeToNuc old.scr CleanMSA RemoveGaps old.scr CT_Species AddSpecies old.scr CloseGF CloseGrid old.scr ColorMap GetColorMap old.scr ColorTree CreateColoredTree old.scr Complement GetComplement old.scr CompressGF CompressGrid old.scr ConvertSP SpToDarwin old.scr ConvertToDF DbToDarwin old.scr CreateDB CreateAcGrid old.scr CreateGF CreateGrid old.scr DF DB old.scr DMDMS CreateDayMatrices old.scr DnaFile database old.scr DNAPepDayhoffM ApproxDnaDayMatrix old.scr Dayhoff CreateOrigDayMatrix old.scr DayhoffM CreateDayMatrix old.scr DelFixed FixedDel old.scr DelIncr IncDel old.scr DigestSeqs DigestSeq old.scr Distribution DrawDistribution old.scr DnaFile database old.scr DotPlot DarwDotplot old.scr DynProgr DynProg old.scr ERROR error old.scr EndOverlayPlot StopOverlayPlot old.scr Entries Entry old.scr Entropy FindEntropy old.scr EntryInfo GetEntryInfo old.scr EntryNumber GetEntryNumber old.scr EqradTree DrawEqualRadialTree old.scr ExponFit ExpFit old.scr ExpFit2 BoundedExpFit old.scr ExtCallFrame CreateCProgram old.scr FlushGF FlushGrid old.scr FragSearch SearchFrag old.scr GetBetween GetLcaSubtree old.scr GetIndex FindTreeFitIndex old.scr GetLabels GetTreeLabels old.scr GetMatchSequence GetAlignSequences old.scr GetTreeLength TotalTreeDistance old.scr GetPath GetPathDistance old.scr GridFile grid old.scr Histogram DrawHistogram old.scr IDS ID old.scr IPCconnect ConnectTcp old.scr IPCdisconnect DisconnectTcp old.scr IPCread ReadTcp old.scr IPCreceive ReceiveTcp old.scr IPCsend SendTcp old.scr IPCreceiveDATA ReceiveDataTcp old.scr IPCsendDATA SendDataTcp old.scr IndexSP CreateSpGrid old.scr LabelTree ChangeLeafLabels old.scr LarsonTree DarwUnrootedTree old.scr LeafNames GetLeafLabels old.scr LinRegr LinearRegression old.scr LinearIntron CreateLinearIntron old.scr LinearIntron0 CreateLinearZeroIntron old.scr LinearIntron1 CreateLinearProbIntron old.scr LoadFile ReadDb old.scr LongestRep FindLongestRep old.scr MAlignment MultiAlign old.scr MachineUsage GetMachineUsage old.scr MapGF MapGrid old.scr MassDyn DynProgMass old.scr MassDynAll DynProgMassDb old.scr MassProfile SearchMassDb old.scr Maximize MaximizeFunc old.scr MinSqTree MinSquareTree old.scr Minimize MinimizeFunc old.scr Minimize2D Minimize2DFunc old.scr Minimizex DisconMinimize old.scr MolWeight GetMolWeight old.scr MostFrequent GetMostFrequentGrams old.scr MoveGap MoveGap old.scr MultAlign CreateMultiAlign old.scr NewArray CreateArray old.scr NewString CreateString old.scr NextGF GetNextGrid old.scr NPAlignMatch AlignNucPepMatch old.scr NPAllMatches GetAllNucPepMatches old.scr NPBackDynProgr NucPepBackDynProg old.scr NPBestPamMatch FindNucPepPam old.scr NPBestPamShake LocalNucPepAlignBestPam old.scr NPDynProgr NucPepDynProg old.scr NPMatch NucPepMatch old.scr NPMultiAllMatches ParallelAllNucPepMatches old.scr NPOneAllMatch AlignNucPepAll old.scr NPRefine GlobalNucPepAlign old.scr NPRefineShake LocalNucPepAlign old.scr NPRegions NucPepRegions old.scr NPSprintMatch DynProgNucPepString old.scr Offsets Offset old.scr OneAllMatch AlignOneAll old.scr OpenGF OpenGrid old.scr OrderedSearch SearchOrderedArray old.scr PA IntToA old.scr PAAA IntToAAA old.scr PAmino IntToAmino old.scr PB IntToN old.scr PBBB IntToNuc old.scr PBase IntToNucleic old.scr PItoPam PerIdentToPam old.scr PamtoPI PamToPerIdent old.scr ParExec ParExecute old.scr ParExec2 ParExecuteSmall old.scr ParTest ParExecuteTest old.scr PatEntries PatEntry old.scr PepPepSearch SearchPepAll old.scr PhyloTree CreatePhyloTree old.scr PickTree FindLabeledSubtree old.scr PlotPam DrawSimPam old.scr PlotOptions Plot old.scr PosInfo GetPosition old.scr PositionDF GetOffset old.scr PrintSeqsInTree PrintTreeSeq old.scr ProbDynProgr ProbDynProg old.scr ProfileEnter EnterProfile old.scr ProfileExit ExitProfile old.scr QueryAll AllQueryGrid old.scr QueryGF QueryGrid old.scr RETURN return old.scr RandTree CreateRandMultAlign old.scr RandomPermut CreateRandPermutation old.scr RandomSeq CreateRandSeq old.scr RandomTrees CreateRandTrees old.scr Refine GlobalAlign old.scr RefineLog LogDelLocalRefine old.scr RefineShake LocalAlign old.scr SameTree IdenticalTrees old.scr Scale DayMatrixScale old.scr SearchDF SearchDb old.scr SearchPepDF SearchSeqTagDb old.scr SearchText CaseSearchString old.scr SelfMatch GetSelfAlign old.scr Sequences Sequence old.scr ShortestPath ConShortestPath old.scr ShortestPath2 ShortestPath old.scr Smooth SmoothData old.scr SplatTree DrawSplatTree old.scr SprintMatch DynProgStrings old.scr Ssystem TimedCallSystem old.scr StackedBar DrawStackedBar old.scr Stats Stat old.scr string name old.scr Strings String old.scr SummarizeTree CollapseNodes old.scr TSP ComputeTSP old.scr TSP3 ComputeCubicTSP old.scr TSP4 ComputeQuadraticTSP old.scr TreeOrder FindCircularOrder old.scr TrulyRandom SetRandSeed old.scr UUUP GenCodeToInt old.scr UnCompressGF UncompressGrid old.scr UnLabelTree UnlabelLeaves old.scr UnionStats UnionStat old.scr View ViewPlot old.scr Violations FindSpeciesViolations old.scr WriteMSA WriteMsa old.scr anitparallel GetAntiparallel old.scr appendto AppendFile old.scr clearw ClearStat old.scr currentOfs CurrentOff old.scr dpuTime DpuTime old.scr eigenvalues Eigenvalues old.scr externcall CallExternal old.scr findkey FindKey old.scr function uneval old.scr gausselim GaussElim old.scr gcm GenCode old.scr kGramRegion GramRegion old.scr kGramRegionScore GetGramRegionScore old.scr kGramSite GramSite old.scr kGramSiteScore GetGramSiteScore old.scr load ReadLibrary old.scr numeric real old.scr plot DrawPlot old.scr srand SetRand old.scr rand Rand old.scr read ReadProgram old.scr readBRK ReadBrk old.scr readDSSP ReadDssp old.scr readfile ReadRawFile old.scr readpipelines OpenPipe old.scr readstat ReadLine old.scr readstatAt ReadOffsetLine old.scr searchtext SearchString old.scr specfunc specuneval old.scr srand SetSeed old.scr string name old.scr system CallSystem old.scr text string old.scr update UpdateStat old.scr writeto WriteFile old.scr Predict PredictSecStruct old.scr NDF NucDB old.scr Simil Sim old.scr string symbols old.scr Text string old.scr PDF PepDB old.scr MaxSimil MaxSim old.scr MinSimil MinSim old.scr GetPam FindBestPam old.scr Entries_print Entry_print old.scr Entries_Offsets Entry_Offset old.scr Entries_Strings Entry_String old.scr Entries_Sequences Entry_Sequence old.scr Entries_Match Entry_Match old.scr Entries_select Entry_select old.scr Offsets_Entries Offset_Entry old.scr Offsets_PatEntries Offset_PatEntry old.scr Offsets_print Offset_print old.scr Offsets_Sequences Offset_Sequence old.scr Offsets_Strings Offset_String old.scr Offsets_Match Offset_Match old.scr PatEntries_Entries PatEntry_Entry old.scr PatEntries_Offsets PatEntry_Offset old.scr PatEntries_Strings PatEntry_String old.scr PatEntries_print PatEntry_print old.scr PatEntries_Sequences PatEntry_Sequence old.scr PatEntries_Match PatEntry_Match old.scr Sequences_Entries Sequence_Entry old.scr Sequences_Offsets Sequence_Offset old.scr Sequences_PatEntries Sequence_PatEntry old.scr Sequences_print Sequence_print old.scr Sequences_Strings Sequence_String old.scr Sequences_Match Sequence_Match old.scr Match_Offsets Match_Offset old.scr Match_Entries Match_Entry old.scr Match_Strings Match_String old.scr Entries_IDS Entry_ID old.scr Match_IDS Match_ID old.scr Sequences_IDS Sequence_ID old.scr Offsets_IDS Offset_ID old.scr PatEntries_IDS PatEntry_ID old.scr IDS_Offsets ID_Offset old.scr IDS_Entries ID_Entry old.scr IDS_Match ID_Match old.scr IDS_Sequences ID_Sequence old.scr Entries_ACS Entry_AC old.scr IDS_Entries ID_Entry old.scr IDS_Match ID_Match old.scr IDS_Sequences ID_Sequence old.scr IDS_Strings ID_String old.scr Match_ACS Match_AC old.scr Entries_ACS Entry_AC old.scr Offsets_ACS Offset_AC old.scr Sequences_ACS Sequence_AC old.scr PatEntries_ACS PatEntry_AC old.scr IDS_Offsets ID_Offset old.scr IDS_Entries ID_Entry old.scr IDS_Match ID_Match old.scr IDS_Sequences ID_Sequence old.scr Entries_ACS Entry_AC old.scr IDS_Entries ID_Entry old.scr IDS_Match ID_Match old.scr IDS_Sequences ID_Sequence old.scr IDS_Strings ID_String old.scr Match_ACS Match_AC old.scr Entries_ACS Entry_AC old.scr Offsets_ACS Offset_AC old.scr Sequences_ACS Sequence_AC old.scr PatEntries_ACS PatEntry_AC old.scr ACS_Offsets AC_Offset old.scr ACS_Entries AC_Entry old.scr ACS_Match AC_Match old.scr ACS_Sequences AC_Sequence old.scr ACS_Strings AC_String old.scr IDS_ACS ID_AC old.scr ACS_IDS AC_ID old.scr NPMatch_type NucPepMatch_type old.scr NPMatch_select NucPepMatch_select old.scr NPMatch_Entries NucPepMatch_Entry old.scr NPMatch_IDS NucPepMatch_ID old.scr NPMatch_print NucPepMatch_print old.scr Stats_select Stat_select old.scr Stats_print Stat_print old.scr Text string