ReadMeFirst.rtf

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{\f673\fbidi \fnil\fcharset238\fprq2 Times CE{\*\falt Times};}{\f674\fbidi \fnil\fcharset204\fprq2 Times Cyr{\*\falt Times};}{\f676\fbidi \fnil\fcharset161\fprq2 Times Greek{\*\falt Times};}{\f677\fbidi \fnil\fcharset162\fprq2 Times Tur{\*\falt Times};}
{\f678\fbidi \fnil\fcharset177\fprq2 Times (Hebrew){\*\falt Times};}{\f679\fbidi \fnil\fcharset178\fprq2 Times (Arabid){\*\falt Times};}{\f680\fbidi \fnil\fcharset186\fprq2 Times Baltic{\*\falt Times};}
{\f681\fbidi \fnil\fcharset163\fprq2 Times (Vietnamese){\*\falt Times};}{\f673\fbidi \fnil\fcharset238\fprq2 Times CE{\*\falt Times};}{\f674\fbidi \fnil\fcharset204\fprq2 Times Cyr{\*\falt Times};}
{\f676\fbidi \fnil\fcharset161\fprq2 Times Greek{\*\falt Times};}{\f677\fbidi \fnil\fcharset162\fprq2 Times Tur{\*\falt Times};}{\f678\fbidi \fnil\fcharset177\fprq2 Times (Hebrew){\*\falt Times};}
{\f679\fbidi \fnil\fcharset178\fprq2 Times (Arabid){\*\falt Times};}{\f680\fbidi \fnil\fcharset186\fprq2 Times Baltic{\*\falt Times};}{\f681\fbidi \fnil\fcharset163\fprq2 Times (Vietnamese){\*\falt Times};}
{\flomajor\f31508\fbidi \fnil\fcharset238\fprq2 Arial CE;}{\flomajor\f31509\fbidi \fnil\fcharset204\fprq2 Arial Cyr;}{\flomajor\f31511\fbidi \fnil\fcharset161\fprq2 Arial Greek;}{\flomajor\f31512\fbidi \fnil\fcharset162\fprq2 Arial Tur;}
{\flomajor\f31513\fbidi \fnil\fcharset177\fprq2 Arial (Hebrew);}{\flomajor\f31514\fbidi \fnil\fcharset178\fprq2 Arial (Arabid);}{\flomajor\f31515\fbidi \fnil\fcharset186\fprq2 Arial Baltic;}
{\flomajor\f31516\fbidi \fnil\fcharset163\fprq2 Arial (Vietnamese);}{\fdbmajor\f31520\fbidi \fnil\fcharset0\fprq2 \'82\'6c\'82\'72 \'83\'53\'83\'56\'83\'62\'83\'4e Western;}
{\fdbmajor\f31518\fbidi \fnil\fcharset238\fprq2 \'82\'6c\'82\'72 \'83\'53\'83\'56\'83\'62\'83\'4e CE;}{\fdbmajor\f31519\fbidi \fnil\fcharset204\fprq2 \'82\'6c\'82\'72 \'83\'53\'83\'56\'83\'62\'83\'4e Cyr;}
{\fdbmajor\f31521\fbidi \fnil\fcharset161\fprq2 \'82\'6c\'82\'72 \'83\'53\'83\'56\'83\'62\'83\'4e Greek;}{\fdbmajor\f31522\fbidi \fnil\fcharset162\fprq2 \'82\'6c\'82\'72 \'83\'53\'83\'56\'83\'62\'83\'4e Tur;}
{\fdbmajor\f31525\fbidi \fnil\fcharset186\fprq2 \'82\'6c\'82\'72 \'83\'53\'83\'56\'83\'62\'83\'4e Baltic;}{\fhimajor\f31528\fbidi \fnil\fcharset238\fprq2 Calibri CE;}{\fhimajor\f31529\fbidi \fnil\fcharset204\fprq2 Calibri Cyr;}
{\fhimajor\f31531\fbidi \fnil\fcharset161\fprq2 Calibri Greek;}{\fhimajor\f31532\fbidi \fnil\fcharset162\fprq2 Calibri Tur;}{\fhimajor\f31535\fbidi \fnil\fcharset186\fprq2 Calibri Baltic;}
{\fhimajor\f31536\fbidi \fnil\fcharset163\fprq2 Calibri (Vietnamese);}{\fbimajor\f31538\fbidi \fnil\fcharset238\fprq2 Times CE{\*\falt Times};}{\fbimajor\f31539\fbidi \fnil\fcharset204\fprq2 Times Cyr{\*\falt Times};}
{\fbimajor\f31541\fbidi \fnil\fcharset161\fprq2 Times Greek{\*\falt Times};}{\fbimajor\f31542\fbidi \fnil\fcharset162\fprq2 Times Tur{\*\falt Times};}{\fbimajor\f31543\fbidi \fnil\fcharset177\fprq2 Times (Hebrew){\*\falt Times};}
{\fbimajor\f31544\fbidi \fnil\fcharset178\fprq2 Times (Arabid){\*\falt Times};}{\fbimajor\f31545\fbidi \fnil\fcharset186\fprq2 Times Baltic{\*\falt Times};}{\fbimajor\f31546\fbidi \fnil\fcharset163\fprq2 Times (Vietnamese){\*\falt Times};}
{\flominor\f31548\fbidi \fnil\fcharset238\fprq2 Times CE{\*\falt Times};}{\flominor\f31549\fbidi \fnil\fcharset204\fprq2 Times Cyr{\*\falt Times};}{\flominor\f31551\fbidi \fnil\fcharset161\fprq2 Times Greek{\*\falt Times};}
{\flominor\f31552\fbidi \fnil\fcharset162\fprq2 Times Tur{\*\falt Times};}{\flominor\f31553\fbidi \fnil\fcharset177\fprq2 Times (Hebrew){\*\falt Times};}{\flominor\f31554\fbidi \fnil\fcharset178\fprq2 Times (Arabid){\*\falt Times};}
{\flominor\f31555\fbidi \fnil\fcharset186\fprq2 Times Baltic{\*\falt Times};}{\flominor\f31556\fbidi \fnil\fcharset163\fprq2 Times (Vietnamese){\*\falt Times};}{\fdbminor\f31560\fbidi \fnil\fcharset0\fprq2 \'82\'6c\'82\'72 \'96\'be\'92\'a9 Western;}
{\fdbminor\f31558\fbidi \fnil\fcharset238\fprq2 \'82\'6c\'82\'72 \'96\'be\'92\'a9 CE;}{\fdbminor\f31559\fbidi \fnil\fcharset204\fprq2 \'82\'6c\'82\'72 \'96\'be\'92\'a9 Cyr;}
{\fdbminor\f31561\fbidi \fnil\fcharset161\fprq2 \'82\'6c\'82\'72 \'96\'be\'92\'a9 Greek;}{\fdbminor\f31562\fbidi \fnil\fcharset162\fprq2 \'82\'6c\'82\'72 \'96\'be\'92\'a9 Tur;}
{\fdbminor\f31565\fbidi \fnil\fcharset186\fprq2 \'82\'6c\'82\'72 \'96\'be\'92\'a9 Baltic;}{\fhiminor\f31568\fbidi \fnil\fcharset238\fprq2 Cambria CE;}{\fhiminor\f31569\fbidi \fnil\fcharset204\fprq2 Cambria Cyr;}
{\fhiminor\f31571\fbidi \fnil\fcharset161\fprq2 Cambria Greek;}{\fhiminor\f31572\fbidi \fnil\fcharset162\fprq2 Cambria Tur;}{\fhiminor\f31575\fbidi \fnil\fcharset186\fprq2 Cambria Baltic;}
{\fhiminor\f31576\fbidi \fnil\fcharset163\fprq2 Cambria (Vietnamese);}{\fbiminor\f31578\fbidi \fnil\fcharset238\fprq2 Times CE{\*\falt Times};}{\fbiminor\f31579\fbidi \fnil\fcharset204\fprq2 Times Cyr{\*\falt Times};}
{\fbiminor\f31581\fbidi \fnil\fcharset161\fprq2 Times Greek{\*\falt Times};}{\fbiminor\f31582\fbidi \fnil\fcharset162\fprq2 Times Tur{\*\falt Times};}{\fbiminor\f31583\fbidi \fnil\fcharset177\fprq2 Times (Hebrew){\*\falt Times};}
{\fbiminor\f31584\fbidi \fnil\fcharset178\fprq2 Times (Arabid){\*\falt Times};}{\fbiminor\f31585\fbidi \fnil\fcharset186\fprq2 Times Baltic{\*\falt Times};}{\fbiminor\f31586\fbidi \fnil\fcharset163\fprq2 Times (Vietnamese){\*\falt Times};}}
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{\operator  David Maddison}{\creatim\yr2018\mo1\dy21\hr10\min29}{\revtim\yr2018\mo1\dy21\hr10\min29}{\version3}{\edmins2}{\nofpages5}{\nofwords2168}{\nofchars12362}{\nofcharsws14501}{\vern50055}{\*\saveprevpict}}{\*\xmlnstbl {\xmlns1 http://schemas.micros
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\ltrch\fcs0 \b\f670\fs48\insrsid8597069 MacClade 4.}{\rtlch\fcs1 \ab\af670\afs48 \ltrch\fcs0 \b\f670\fs48\insrsid4087784 09 Beta}{\rtlch\fcs1 \ab\af670\afs48 \ltrch\fcs0 \b\f670\fs48\insrsid8597069 
\par 
\par }\pard \ltrpar\ql \li0\ri0\nowidctlpar\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\wrapdefault\faauto\rin0\lin0\itap0\pararsid4087784 {\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\insrsid8597069 This is a }{
\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\insrsid4087784 beta}{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\insrsid8597069  version of MacClade}{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\insrsid4087784  from 
2011 that was never released.  Below is the \u8220\'d2ReadMe\u8221\'d3 file from MacClade 4.08.  
\par 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid4087784 The version of this source posted in January 2018}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid4087784  will not run on MacOS X Lion (10.7) or any later MacOS.
\par }\pard \ltrpar\ql \li0\ri0\nowidctlpar\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\insrsid8597069 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\insrsid8597069 Hardware and system software requirements
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\insrsid8597069 MacOS
\par }{\rtlch\fcs1 \ab\ai\af672 \ltrch\fcs0 \b\i\f672\insrsid8597069 Computer:}{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\insrsid8597069  }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 
any Macintosh that can run System 7.5 or later, including MacOS X (e.g., PowerMacs, PowerMac G3, PowerMac G4, PowerMac G5, iMacs, Powerbooks, iBooks, Quadras, Centris, and Performas, among others).}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid4087784  }{
\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid4087784 
\par }{\rtlch\fcs1 \ab\ai\af672 \ltrch\fcs0 \b\i\f672\insrsid8597069 Hard disk and CD drive:}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069  required.
\par 
\par }{\rtlch\fcs1 \ab\ai\af672 \ltrch\fcs0 \b\i\f672\insrsid8597069 Memory (RAM):}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 
 depends on your data and tree files. For example, with 4Mb or more of RAM devoted to MacClade, it should be able to handle 200 taxa and 500 characters in a morphological matrix, or 50 taxa and 2000 charact
ers of DNA sequence. More memory is required if some of the tools for molecular sequence editing are used.
\par 
\par }{\rtlch\fcs1 \ab\ai\af672 \ltrch\fcs0 \b\i\f672\insrsid8597069 Printer: }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 
any Macintosh-compatible printer (e.g., ink jet, laser); how-ever, some of MacClade's tree-printing features require a PostScript\u174\'a8 printer.
\par 
\par }{\rtlch\fcs1 \ab\ai\af672 \ltrch\fcs0 \b\i\f672\insrsid8597069 System:}{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\insrsid8597069  }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 System 7.5 or later; compatible with Systems 8, 9, and OS X.   
\par 
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\insrsid8597069 Windows\u174\'a8
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 MacClade 4 can also run on a computer using the Microsoft Windows\u174\'a8 operating system within a MacOS emulator, as discussed under "Using MacClade under Microsoft Windows\u174\'a8", below.
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\insrsid8597069 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\insrsid8597069 Installing MacClade
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\insrsid8597069 MacOS
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 
MacClade and associated files are distributed in folders contained on this CD.  To install MacClade on a MacOS computer, drag the files needed from the CD on to your hard disk.  We suggest you copy both the program and docu
mentation onto your hard drive. If you copy the documentation, copy the entire MacClade Manual folder, otherwise the movies and example files will work be available.
\par 
\par }{\rtlch\fcs1 \ab\ai\af672 \ltrch\fcs0 \b\i\f672\insrsid8597069 Program}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 : There are three versions of MacClade on the CD, whose names end in "OS X", "PPC"
, and "68K" respectively.  Copy onto your hard disk the OS X version if you are running MacOS X.  Copy instead the PPC (PowerPC) version if you have a modern Macintosh (any with a PowerPC/G3/G4 processor) but are running MacOS 7.5 through 9.2.  Copy onto 
your hard disk the 68K version if you have an older Macintosh model using 68020, 68030, or 68040 processors (e.g., IIci, Quadra and Centris).
\par 
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\insrsid8597069 WARNING}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 : The method used by MacClade to personalize your copy may conflict with some system extensions. We current
ly know of one conflict: you will not be able to successfully install and start MacClade the first time if you have the CleverContent extensions enabled on your computer.  If you have difficulty starting MacClade, then restart your Macintosh, and hold dow
n
 the Shift key as the computer is restarting.  This will turn off extensions.  Reinstall and restart MacClade.  When asked to personalize your copy of MacClade, do so, and then quit MacClade. Once you have successfully started and personalized MacClade, y
ou should be able to restart the Macintosh normally (without the Shift key held down) and then use MacClade.  
\par  
\par }{\rtlch\fcs1 \ab\ai\af672 \ltrch\fcs0 \b\i\f672\insrsid8597069 Documentation and examples}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 : The MacClade manual, supplement, and folders of movies and example files are in the "MacClade Manua
l" folder on the CD.  Drag the entire folder to your hard disk if you wish quick access to the documentation.
\par 
\par There are also classroom versions of MacClade in the MacClade Classroom Version folder. Install these on a computer by simply dragging the appropriate copy (OS X, PowerPC, or 68K) onto the computer's hard disk.
\par 
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\insrsid8597069 Windows\u174\'a8
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 Installation will may vary depending on the MacOS emulator used.  Instructions for installation with the Executor emulator are given under "Using MacClade under Microsoft Windows\u174\'a8".
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\insrsid8597069 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\insrsid8597069 Updates
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\insrsid8597069 You should regularly check MacClade's World Wide Web site
\par 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://macclade.org
\par 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 as at this site we will post files that will update your copy of MacClade 4 to the latest version.
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\ulc17\insrsid8597069 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\ulc17\insrsid8597069 Installing Acrobat Reader
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 In order to be able to read the MacClad
e 4 manual and supplement, you will need to have an application installed that can read Portable Document Format (PDF) files, such as Adobe Acrobat Reader. A copy of Acrobat Reader for the MacOS is included on this CD; if you do not have Acrobat Reader on
 your computer, please install it by running the installer included on the CD. 
\par 
\par The MacClade manual is very large, and may require that you increase the amount of memory available to Acrobat Reader.  }{\rtlch\fcs1 \ab\ai\af672 \ltrch\fcs0 \b\i\f672\ulc17\insrsid8597069 If you encounter problems reading the manual}{\rtlch\fcs1 \af671 
\ltrch\fcs0 \f671\ulc17\insrsid8597069 , increase t
he amount of memory available to Acrobat Reader by selecting Acrobat reader in the Finder, and choosing Get Info from the File menu.  In the window that appears, go to the Memory panel, and increase the Preferred Size for Acrobat Reader by several megabyt
es.
\par 
\par If the version of Acrobat Reader provided on the CD is not suitable for your computer, or you wish to see if there is a newer version, check out Adobe's World Wide Web site at }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 
http://www.adobe.com}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 .
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\ulc17\insrsid8597069 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\ulc17\insrsid8597069 Problems running MacClade? 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 MacClade has been extensi
vely tested, but in any program this large there will remain bugs.  If MacClade seems to be giving you incorrect results in its phylogenetic calculations or in storing your data, then please attempt to understand the problem, learn how to reproduce it, an
d contact us at  }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\ulc17\insrsid8597069 clade@arizona.edu}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 
 with a bug report.  If MacClade appears the be crashing your computer, then please attempt to determine if MacClade is the culprit, learn how to reproduce it, and send us a bug report. Before sending us a bug report, pleas
e refer to the section "Reporting bugs" in the "Introduction" chapter of the manual.
\par 
\par MacClade's World Wide Web site (}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://macclade.org}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 
) has the latest information on compatibilities and bugs. Updated versions will be posted as bug fixes are made.
\par 
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\ulc17\insrsid8597069 Not enough memory for MacClade?
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 
One possible cause of crashing is that too little memory has been allocated to MacClade. The memory needed depends upon the data format, number of stored trees, presence of pictures, what calculations are requested, and other f
actors. MacClade's memory use is discussed in the section "Computer memory and MacClade's limits" in the chapter "Getting started with MacClade" of the manual.
\par 
\par If you are running MacOS X, memory is automatically assigned to MacClade as needed.  However, i
f you are running MacOS 9 or earlier, you need to manually set how much memory MacClade has available.  In MacOS 9 or earlier, to allocate more memory to MacClade,  select MacClade's icon (make sure it is not running!) in the Finder, choose }{\rtlch\fcs1 
\ab\af670 \ltrch\fcs0 \b\f670\ulc17\insrsid8597069 Get Info}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069  under the }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\ulc17\insrsid8597069 File}{\rtlch\fcs1 \af671 \ltrch\fcs0 
\f671\ulc17\insrsid8597069  menu, and edit the Preferred Size under the Memory panel. The next time you start up MacClade, the MacOS will reserve this larger amount of memory for MacClade. 
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\ulc17\insrsid8597069 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\ulc17\insrsid8597069 Using MacClade under Microsoft Windows\u174\'a8 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 MacClade is a MacOS program, designed to run on an Apple Macintosh computer.   There exist several programs that emulate the MacOS on the Microsoft Windows operating system, including Executor (}
{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://www.ardi.com/}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 ), SoftMac 2000 (}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 
http://www.emulators.com/}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 ), Basilisk II (}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://www.uni-mainz.de/~bauec002/B2Main.html}{\rtlch\fcs1 \af671 \ltrch\fcs0 
\f671\ulc17\insrsid8597069 ), and the vMac Project (}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://www.vmac.org/}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 
).  These would, in principle, allow MacClade to run on Windows computers. 
\par 
\par Of the emulators mentioned, we have personal experience only with ARDI\rquote s Executor (}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://www.ardi.com/}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 ).  It will a
llow you to run the 68K version of MacClade. MacClade runs remarkably well though not perfectly under Executor, and there are limitations and anomalies you may encounter. For the latest information about using MacClade under Executor, see the MacClade web
 site (}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://macclade.org}{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 ).
\par 
\par To install MacClade into the Executor environment, insert the MacClade CD into the computer. In the Program folder will be two copies of MacClade: mc68k.hqx is a bin-hexed archive that contains the 68K ver-sion of MacClade; mcp
pc.hqx contains the PowerPC version. They also contain the example files. Copy the file mc68k.hqx file to the App directory in the directory containing Executor.  Start up Executor; within Executor, start up Stuffit Expander. In Stuffit Expander, open the
 file mc68.hqx. This will unstuff the archive, and  you will be left with a directory containing MacClade and the examples in your App direc-tory.  You will then be ready to start MacClade from within Executor.
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\ulc17\insrsid8597069 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\ulc17\insrsid8597069 Electronic mail and World Wide Web addresses
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\ulc17\insrsid8597069 Registration
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 Make sure you register your copy of MacClade.  The registration page is at
\par 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://www.sinauer.com/macclade/register.htm
\par 
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\ulc17\insrsid8597069 Technical support
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 For technical support (including bug reports) please use the electronic mail address clade@arizona.edu.
\par 
\par }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\ulc17\insrsid8597069 News, information and updates
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 MacClade's World Wide Web site is at
\par 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ul\cf17\ulc17\insrsid8597069 http://macclade.org
\par 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 This site contains general information about MacClade, information
 about bugs, frequently asked ques-tions and answers, and so on.  At times there may be files posted which you can download to update your copy of MacClade.
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\ulc17\insrsid8597069 
\par 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\ulc17\insrsid8597069 How to cite MacClade 
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 MacClade serves as a calculating tool and yet it also contains new ideas, i
mplicit suggestions, and new methods.  Use of ideas in this manual or in MacClade should be acknowledged as with any other published paper. MacClade should also be cited in your Materials and Methods as a source of the calculations or output used in your 
papers. }{\rtlch\fcs1 \ab\af670 \ltrch\fcs0 \b\f670\ulc17\insrsid8597069  }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 We recommend a citation like the following, which can be used both for the program and this accompanying manual:
\par 
\par Maddison, D. R. and W. P. Maddison, 2005. MacClade 4: Analysis of phylogeny and character evolution. Version 4.08. Sinauer Associates, Sunderland, Massachusetts. 
\par 
\par Note that the version you receive on disk may be a more recent one than 4.08, or you may have updated MacClade using an updater available from MacClade's web site.  You should therefore alter the citation if appropriate to inc
lude the number and date of the version you used.  The version number and date should be evident from the About MacClade window within MacClade. 
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\ulc17\insrsid8597069 
\par }{\rtlch\fcs1 \ab\af670\afs36 \ltrch\fcs0 \b\f670\fs36\ulc17\insrsid8597069 Learning how to use MacClade and contents of the manual
\par }{\rtlch\fcs1 \af671 \ltrch\fcs0 \f671\ulc17\insrsid8597069 The manual for MacClade is present on this CD, as a P
DF file.  You can print out the manual, or examine it on your computer.  We strongly recommend that you examine the manual, not only to answer questions you might have, but also to discover aspects of MacClade with which you are unfamiliar.  It is likely 
that you would thereby discover tools in MacClade that would be valuable to you.
\par 
\par MacClade is a large and complex program. If you are just getting started with MacClade, we advise you to follow through the examples in Chapter 2 of the manual, "A Tutorial Ov
erview of MacClade". This will guide you step by step through simple data files, and thereby introduce you to some of the basic functions of MacClade.
\par 
\par Chapters 3 and 4 concern phylogenetic theory.  Chapter 3, "Overview of Phylogenetic Inference", defines 
terms of relevance to MacClade, discusses methods of inference of phylogenies, and of patterns and processes of character evolution. Chapter 4, "Reconstructing Character Evolution Using Parsimony", describes the assumptions and methods MacClade uses in re
constructing character evolution. We recommend that you read the relevant sections of these chapters before using MacClade to study character evolution.  
\par 
\par Chapters 5 through 25 of this manual provide more detailed guidance about using MacClade. Although we
 hope that many of MacClade's features will be obvious from the program itself, some important ones will not. So that you may discover these features, and thoroughly understand MacClade's analyses, we strongly recommend that you at least glance through Ch
apters 5 through 25.
\par 
\par Chapters 5 through 10 introduce some basics of using MacClade. "Getting Started with MacClade" gives an overview of hardware and software requirements, installation, memory management, and setting preferences.  "Managing Data Files" te
lls how to create, open, and save data files. "NEXUS Files and Blocks" describes how to select options for saving NEXUS files, and how to manage NEXUS blocks. "Importing and Exporting Text Files" describes how to share files with Clustal, NONA, PHYLIP, an
d
 other programs, as well as import and export files in NBRF, Genbank, GCG/MSF, and other formats.  "MacClade's Windows" introduces the windows of MacClade, including the data editor window, the tree window, and the list windows.  "List Windows" explains h
ow items like taxa, characters, and trees can be manipulated using the list windows. 
\par 
\par Chapter 11, "Taxa",  describes how observed taxa are created and manipulated.  Taxa are the basic units with which characters are associated (via data matrices) and whose relationships are shown by trees.
\par 
\par Chapters 12 through 16 give detailed information about manipulating character data and assumptions. "Characters and Their States" describes MacClade's data formats and how characters and their states can be named and man
ipulated. "Entering and Editing Data" explains the use of MacClade's spreadsheet data editor. "Display of Data" tells how the data editor's display can be adjusted. "Assumptions About Characters" details the various assumptions used in MacClade's calculat
ions, such as weighting of characters and how states transform one to another. "Preparing Molecular Data" focuses on data formats and other issues related to molecular data, including sequence alignment. 
\par 
\par Chapters 17 through 23 describe working with phylogenetic trees and the relationship between character data and the tree.  "Trees and Tree Manipulation" introduces MacClade's tree window, and how trees can be manipulated, stored, and retrieved.  In "Traci
n
g Character Evolution", methods for reconstructing the ancestral states (and thereby pathways of character evolution) are discussed. In "Basic Tree and Character Statistics", simple statistics of treelength and indices such as the consistency index are ou
t
lined. MacClade's charting facility is described in "Charting Tree and Character Statistics". Use of continuous-valued characters is explained in "Continuous Characters". The next chapter discusses "Patterns of Correlated Character Evolution", particularl
y the concentrated-changes test for phylogenetic character correlation. MacClade's randomization facilities, which can be used in various statistical tests, are discussed in "Generating Random Data and Random Trees".
\par 
\par Chapter 24, "Note Keeping" explains how to attach notes and pictures to various parts of the data file.  Chapter 25, "Recording Your Work: Printing, Graphic, and Text Files" gives strategies for keeping records. Printing facilities are described there.

\par 
\par The remaining chapter ("Using MacClade and PAUP* Together") describes how to use MacClade in combination with Swofford's PAUP* program (Swofford, 2001).
\par }{\rtlch\fcs1 \af671\afs20 \ltrch\fcs0 \f671\fs20\ulc17\insrsid8597069 
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