PAUP* 4.0 Beta: Command Reference --Draft Version 3--

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Table of ContentsCommands used in the DISTANCES Block...................................27Dimensions .......................................................................................................................... 28Format................................................................................................................................... 28TaxLabels.............................................................................................................................. 30Matrix.................................................................................................................................... 30Commands used in the PAUP Block...............................................30Options And Subcommands Affecting Multiple Commands..................................... 30?.............................................................................................................................................. 33! .............................................................................................................................................. 33Agree..................................................................................................................................... 33AllTrees................................................................................................................................. 35Ancstates .............................................................................................................................. 36Assume ................................................................................................................................. 36BandB.................................................................................................................................... 37BaseFreqs.............................................................................................................................. 39BootStrap.............................................................................................................................. 39CD.......................................................................................................................................... 42CharPartition ....................................................................................................................... 42CharSet ................................................................................................................................. 42ClearTrees ............................................................................................................................ 43Condense.............................................................................................................................. 43Constraints ........................................................................................................................... 44ConTree ................................................................................................................................ 44CStatus.................................................................................................................................. 47CType.................................................................................................................................... 48Defaults................................................................................................................................. 49Delete .................................................................................................................................... 49DerootTrees.......................................................................................................................... 50DescribeTrees....................................................................................................................... 51DOS ....................................................................................................................................... 53DScores ................................................................................................................................. 53DSet ....................................................................................................................................... 55Edit ........................................................................................................................................ 59Exclude ................................................................................................................................. 60Execute.................................................................................................................................. 60Export.................................................................................................................................... 61ExSet...................................................................................................................................... 62Filter ...................................................................................................................................... 62Factory .................................................................................................................................. 64FStatus .................................................................................................................................. 65GammaPlot .......................................................................................................................... 65GenerateTrees...................................................................................................................... 66GetTrees................................................................................................................................ 67Help....................................................................................................................................... 69HomPart ............................................................................................................................... 70HSearch ................................................................................................................................ 71Include .................................................................................................................................. 762 February, 2002 PAUP* 4.0 beta documentaion
Table of ContentsInGroup ................................................................................................................................ 77JackKnife............................................................................................................................... 77Lake....................................................................................................................................... 79Leave..................................................................................................................................... 81LoadConstr........................................................................................................................... 81Log......................................................................................................................................... 82LScores.................................................................................................................................. 83LSet........................................................................................................................................ 87MatrixRep............................................................................................................................. 92MPRSets................................................................................................................................ 94NJ........................................................................................................................................... 94Outgroup.............................................................................................................................. 96PairDiff ................................................................................................................................. 96Permute ................................................................................................................................ 97Pscores .................................................................................................................................. 98PSet...................................................................................................................................... 101Puzzle.................................................................................................................................. 103Quit ..................................................................................................................................... 105RandTrees .......................................................................................................................... 105RateSet ................................................................................................................................ 106Reconstruct......................................................................................................................... 107Restore ................................................................................................................................ 108RevFilter ............................................................................................................................. 108Reweight............................................................................................................................. 108RootTrees............................................................................................................................ 109SaveAssum......................................................................................................................... 110SaveDist.............................................................................................................................. 111SaveTrees............................................................................................................................ 112Set ........................................................................................................................................ 114ShowAnc ............................................................................................................................ 121ShowCharParts.................................................................................................................. 122ShowConstr........................................................................................................................ 122ShowDist ............................................................................................................................ 122ShowMatrix........................................................................................................................ 123ShowRateSets..................................................................................................................... 123ShowTaxParts .................................................................................................................... 123ShowTrees.......................................................................................................................... 124ShowUserType .................................................................................................................. 124SortTrees............................................................................................................................. 125StarDecomp........................................................................................................................ 125SurfCheck........................................................................................................................... 126TaxPartition........................................................................................................................ 126TaxSet.................................................................................................................................. 127Time .................................................................................................................................... 127ToNEXUS ........................................................................................................................... 127TreeDist .............................................................................................................................. 129TreeInfo .............................................................................................................................. 130TreeWts............................................................................................................................... 131TStatus ................................................................................................................................ 131PAUP* 4.0 beta documentaion February, 2002 3
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Page 8 and 9: Command FormatCommand Referenceyour
Page 10 and 11: Command FormatCommand Reference2411
Page 12 and 13: Commands used in the TAXA BlockComm
Page 14 and 15: Commands used in the CHARACTERS Blo
Page 20 and 21: Commands used in the DATA BlockComm
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Page 24 and 25: Commands used in the SETS BlockComm
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Page 28 and 29: Commands used in the TREES BlockCom
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Page 32 and 33: Commands used in the PAUP BlockComm
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Commands used in the PAUP BlockComm
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Command ReferenceCommands used in t
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ReferencesREFERENCESAdams, E. N., I
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ReferencesHarary, F. 1969. Graph Th
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Referencesdistics 1:186-189.Nei, M.
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PAUP* 4.0 Beta: Command Reference --Draft Version 3--

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