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

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Commands used in the CHARACTERS BlockCommand ReferenceLABELS or NOLABELS for compatibility with other NEXUS programs.LABELS with no other qualifier is equivalent to LABELS = LEFT.Example input format:begin data;dimensions ntax=4 nchar=5;format label = right;matrix00111 taxon10111? taxon211001 taxon310000 taxon4;end;TRANSPOSEIf TRANSPOSE is specified, rows of the data matrix correspond tocharacters and columns correspond to taxa. Otherwise, rowscorrespond to taxa and columns to characters. The following is anexample of a transposed data matrix:begin data;dimensions ntax=4 nchar=5;format transpose;taxlabels taxon1 taxon2 taxon3 taxon4;matrixchar1 0011char2 0110char3 1100char4 1100char5 1?10;end;INTERLEAVESpecification of allows the data to be entered in "blocks" ofcharacters. If the data is not transposed, then each "block" containsinformation for some of the characters, for all taxa. Taxa in eachsection must occur in the same order. This format is especially usefulfor molecular sequence data, where the number of characters can belarge. A small interleaved matrix follows:matrixtaxon1taxon2taxon3taxon4A C C T C G G CA C C T C G G CA C G T C G C TA C G T C G C T14 February, 2002 PAUP* 4.0 beta documentation
Command ReferenceCommands used in the CHARACTERS Blocktaxon1 T T A A C G Ataxon2 T T A A C C Ataxon3 C T C A C C Ataxon4 T T C A C C A;The interleaved sections need not all be of the same length. In aninterleaved matrix, new line characters are significant; they indicatethat the next character information encountered applies to a differenttaxon (for non-transposed matrices).[NO]TOKENSThe TOKENS subcommand is currently not supported by PAUP* 4.0beta; however, this subcommand is described here because it will besupported in the final release 4.0. This subcommand specifieswhether or not data matrix entries are single symbols, or can betokens. If TOKENS is specified, then the data values must be fullNEXUS tokens, separated by whitespace or punctuation asappropriate, as in the following example:begin characters;dimensions nchar=3;format tokens;matrixtaxon_1 absent red bigtaxon_2 absent blue smalltaxon_3 present blue small;end;[NO]TOKENS is the default and is not allowed for DATATYPES DNA,RNA, and NUCLEOTIDE. If TOKENS is invoked, the standard 3-letteramino acid abbreviations can be used with DATATYPE = PROTEIN,and defined state names for DATATYPE = STANDARD.ELIMINATEThis command allows one to specify a list of characters that are to beexcluded from consideration. PAUP* will completely ignore eliminatedcharacters. (This is similar to the ZAP subcommand in version 3.1 of PAUP.)For example;eliminate 4-100;tells the program to skip over characters 4 through 100 when the matrix isread. Character-set names are not allowed in the character list. Thiscommand does not affect character numbers.PAUP* 4.0 beta documentation February, 2002 15
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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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