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

Commands used in the DISTANCES BlockCommand Referencedefines taxon labels and ordering (e.g., TAXA). The syntax of the block is asfollows:BEGIN DISTANCES;[ DIMENSIONS [ NEWTAXA ] NTAX = number-of-taxaNCHAR = number-of-characters;][ FORMAT[ TRIANGLE = { LOWER | UPPER | BOTH } ][ [NO] DIAGONAL ][ [NO] LABELS ][ MISSING = SYMBOL ][ INTERLEAVE ] ; ][ TAXLABELS taxon-name taxon-name...;]MATRIX distance-matrix ;END;Commands must appear in the order listed. Only one of each command isallowed per block.DIMENSIONSThe NTAX subcommand of this command is needed to process the matrixwhen some defined taxa are omitted from the distance matrix. The NCHARsubcommand is optional, and can be used to indicate the number ofcharacters for those analyses that need to know how many characters (ifany) where used to calculate the distances. NCHAR is not required forsuccessful reading of the matrix.As for the CHARACTERS block, taxa can be defined in a DISTANCES block ifNEWTAXA precedes the NTAXA subcommand in the DIMENSIONS command.It is advised that new taxa not be defined in a DISTANCES block, for thereasons discussed in the description of the DATA block. NEWTAXA, ifpresent, must be appear before the NTAX subcommand.FORMATThis command specifies the formatting of the MATRIX. The [NO]LABELS andMISSING subcommands are as described in the CHARACTERS block.TRIANGLE = { LOWER | UPPER | BOTH }This subcommand specifies whether only the lower left half of thematrix is present, or only the upper right, or both halves. Below isone example of an upper triangular matrix and one of a matrix withboth halves included.28 February, 2002 PAUP* 4.0 beta documentation