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

More documents

Recommendations

Info

Table of ContentsTypeSet ............................................................................................................................... 131Undelete ............................................................................................................................. 132UPGMA .............................................................................................................................. 132UserTree ............................................................................................................................. 134UserType ............................................................................................................................ 134Weights............................................................................................................................... 134Wts....................................................................................................................................... 134WtSet................................................................................................................................... 134References .........................................................................................1374 February, 2002 PAUP* 4.0 beta documentaion
Command ReferenceCommand FormatCOMMAND REFERENCEThis document describes the PAUP* command format. Unless statedotherwise, these commands may be included in the PAUP block of aNEXUS file, or typed from the command line. The EDIT command may onlybe issued from the command line. All users will need to be familiar with thecommands available in the TAXA, CHARACTERS, ASSUMPTIONS, SET, TREES,CODON, and DISTANCE blocks, which are normally placed in PAUP inputfiles. In versions of PAUP* that provide a menu-based interface, onlyknowledge of these "block" commands is required, as other instructions toPAUP* can be accomplished through the menu system. Some users,however, may prefer a command-driven interface. Consequently, exceptfor certain machine-specific features, PAUP* may be controlled entirely bya command-line system. Commands may also be placed into input files forconvenience (i.e., to avoid repeated typing of complicated commands) andto provide a simple "batch" facility. If you have no experience using PAUP*,then we recommend reading the Quick Start Tutorial included on yourdistribution disk and also available on the World Wide Web at:http://paup.csit.fsu.edu/downl.htmlCommand FormatThe command descriptions below use some conventions that will be morefully described in subsequent editions of this reference document.Remember that upper-case items are to be entered as shown. Italicizeditems—e.g., user-item—represent variable items to be substituted by theuser. Items inside of square brackets—e.g., [OPTIONAL_ITEM]—areoptional. Items inside of curly braces and separated by vertical bars—e.g.,{ X | Y | Z }—are mutually exclusive options; only one of the choicesindicated may be used. The default item (if any) is underlined, as in { ABC| DEF }. Options in commands are generally specified as "KEYWORD =VALUE" for options that have two or more potential values. For options thatrepresent simple "on-off" ("Boolean") switches, KEYWORD = YES andKEYWORD = NO can be used to select or deselect options, respectively. Also,options may be selected by simply specifying KEYWORD.Each command begins with a command-name and ends with a semicolon.Otherwise, the commands are completely free-format. A command mayspan any number of lines and whitespace (tabs and blanks) may be insertedat will. Input of PAUP* commands is case-insensitive, so you may entercommand names, option keywords, etc., in any combination of upper- andlower-case characters (the only exception pertains to the MATRIXcommand). In addition, PAUP* allows abbreviation of command namesand keywords to the shortest unambiguous truncation. Note that otherNEXUS-conforming programs may not accept these abbreviations.MacClade 3.0, in particular, does not allow abbreviations, so if you wantPAUP* 4.0 beta documentation February, 2002 5
Page 2 and 3: PAUP* 4.0 beta version disclaimer a
Page 4 and 5: Table of ContentsCommands used in t
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
Page 22 and 23: Commands used in the ASSUMPTIONS Bl
Page 24 and 25: Commands used in the SETS BlockComm
Page 26 and 27: Commands used in the SETS BlockComm
Page 28 and 29: Commands used in the TREES BlockCom
Page 30 and 31: Commands used in the DISTANCES Bloc
Page 32 and 33: Commands used in the PAUP BlockComm
Page 56 and 57:
Commands used in the PAUP BlockComm
Page 58 and 59:
Page 60 and 61:
Page 62 and 63:
Page 64 and 65:
Page 66:
Page 69 and 70:
Command ReferenceCommands used in t
Page 71 and 72:
Page 73 and 74:
Page 75 and 76:
Page 77 and 78:
Page 79 and 80:
Page 81 and 82:
Page 83 and 84:
Page 85 and 86:
Page 87 and 88:
Page 89 and 90:
Page 91 and 92:
Page 93 and 94:
Page 95 and 96:
Page 97 and 98:
Page 99 and 100:
Page 101 and 102:
Page 103 and 104:
Page 105 and 106:
Page 107 and 108:
Page 109 and 110:
Page 111 and 112:
Page 113 and 114:
Page 115 and 116:
Page 117 and 118:
Page 119 and 120:
Page 121 and 122:
Page 123 and 124:
Page 125 and 126:
Page 127 and 128:
Page 129 and 130:
Page 131 and 132:
Page 133 and 134:
Page 135 and 136:
Page 137 and 138:
Page 139 and 140:
ReferencesREFERENCESAdams, E. N., I
Page 141 and 142:
ReferencesHarary, F. 1969. Graph Th
Page 143 and 144:
Referencesdistics 1:186-189.Nei, M.
show all

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

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?