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

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Commands used in the ASSUMPTIONS BlockCommand ReferenceOPTIONSThis command houses a number of disparate subcommands. They are all ofthe form subcommand = option.DEFTYPE = type-nameThis specifies the default character type for parsimony analyses.Whenever a character's type is not explicitly stated, its type is takento be the default type. The default DEFTYPE is UNORD , but may bechanged to one of the following: ORD, UNORD, DOLLO, DOLLO.UP,DOLLO.DN, IRREV, IRREV.UP, or IRREV.DN.POLYTCOUNT = { MINSTEPS | MAXSTEPS }This option specifies whether polytomies are treated as "hard" or"soft" (see Maddison (1989)) when counting the number of stepsrequired by a character and when reconstructing ancestral states.PAUP* currently supports only POLYTCOUNT = MAXSTEPS ("hard"polytomies), and will ignore the POLYTCOUNT specification.GAPMODE = { MISSING | NEWSTATE | INDEL }Specifies how gaps are to be treated. GAPMODE = MISSING designatesgaps to be treated in the same way as missing data; GAPMODE =NEWSTATE specifies that gaps are to be treated as an additional state(for DNA/RNA data, as a fifth base).USERTYPE***** Give the predefined character types here. The USERTYPE commanddefines a character transformation type, as used in parsimony analysis todesignate the cost of changes between states. USERTYPES must be definedbefore they are referred to in any TYPESET. Character-type-description mustfollow the rules for character-state tree or stepmatrix description.The STEPMATRIX format is as follows:usertype mymatrix (stepmatrix)=ns s s s. k k kk . k kk k . kk k k .;where n is the number of rows and columns in the step matrix, the s's arestate symbols, and the k's are the cost for going between states. n can takeany value _ 2. Diagonal elements may be listed as periods. If a change is tobe prohibited, then one enters an "i" for infinity. Typically, the state symbolswill be in sequence, but they need not be. The following matrices assignvalues identically:20 February, 2002 PAUP* 4.0 beta documentation
Command ReferenceCommands used in the ASSUMPTIONS Blockusertype mymatrix (stepmatrix)=40 1 2 3. 1 5 11 . 5 15 5 . 51 1 5 .;usertype mymatrix2 (stepmatrix)=42 0 3 1. 5 5 55 . 1 15 1 . 15 1 1 .;The CSTREE format is very similar to the TREE format in a TREES block. Thatis, character state trees are described in the parenthesis notation followingthe rules given for Trees of taxa. Instead of taxon labels, character statesymbols are used. Thususertype cstree-name (cstree) = [(list ofsubtrees)][state-symbol]];where each subtree has the same format as the overall tree and the subtreesare separated by commas.TYPESETA TYPESET specifies a set of character-type assignments for each characteras used in parsimony analysis. Any characters not listed in the charactersethave the default character type. The type names to be used are either thepredefined ones or those defined in a USERTYPE command. Each value in adefinition in VECTOR format must be separated by whitespace. Thefollowing are equivalent type sets:typeset mytypes = Ord: 1 4 6, Unord: 2 3 5;typeset mytypes (vector) = Ord Unord Unord OrdUnord Ord;WTSETA WTSET specifies a set of character-weight assignments for each character.Any characters not listed in the character-set have weight 1. The weightsmay be either integers or real numbers. Each value in a definition inVECTOR format must be separated by whitespace, unless the NOTOKENSoption is invoked, in which case no whitespace is needed, and all weightsmust be integers in the range 0-9. The following are equivalent weight sets:wtset mywts = 3: 1 4 6, 1: 2 3 5;PAUP* 4.0 beta documentation February, 2002 21
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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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