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| 12 | <DIV ALIGN=RIGHT> |
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| 13 | version 3.6 |
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| 14 | </DIV> |
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| 15 | <P> |
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| 16 | <DIV ALIGN=CENTER> |
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| 17 | <H1>DOLMOVE -- Interactive Dollo and Polymorphism Parsimony</H1> |
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| 18 | </DIV> |
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| 19 | </PRE> |
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| 20 | <P> |
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| 21 | © Copyright 1986-2002 by the University of |
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| 22 | Washington. Written by Joseph Felsenstein. Permission is granted to copy |
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| 23 | this document provided that no fee is charged for it and that this copyright |
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| 24 | notice is not removed. |
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| 25 | <P> |
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| 26 | DOLMOVE is an interactive parsimony program which uses the Dollo and |
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| 27 | Polymorphism parsimony criteria. It is inspired on Wayne Maddison and |
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| 28 | David Maddison's marvellous program MacClade, which is written for Apple |
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| 29 | MacIntosh computers. DOLMOVE reads in a data set which is prepared in almost |
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| 30 | the same format as one for the Dollo and polymorhism parsimony program |
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| 31 | DOLLOP. It allows the user to choose an initial tree, and displays this tree |
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| 32 | on the screen. The user can look at different characters and the way their |
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| 33 | states are distributed on that tree, given the most parsimonious reconstruction |
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| 34 | of state changes for that particular tree. The user then can specify how the |
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| 35 | tree is to be rearraranged, rerooted or written out to a file. By looking at |
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| 36 | different rearrangements of the tree the user can manually search for the most |
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| 37 | parsimonious tree, and can get a feel for how different characters are affected |
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| 38 | by changes in the tree topology. |
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| 39 | <P> |
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| 40 | This program is compatible with fewer computer systems than the other |
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| 41 | programs in PHYLIP. It can be adapted to PCDOS systems or to |
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| 42 | any system whose screen or terminals emulate DEC VT100 |
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| 43 | terminals (such as Telnet programs for logging in to remote computers over a |
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| 44 | TCP/IP network, |
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| 45 | VT100-compatible windows in the X windowing system, and any |
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| 46 | terminal compatible with ANSI standard terminals). |
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| 47 | For any other screen types, there is a generic option which does |
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| 48 | not make use of screen graphics characters to display the character |
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| 49 | states. This will be less effective, as the states will be less |
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| 50 | easy to see when displayed. |
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| 51 | <P> |
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| 52 | The input data file is set up almost identically to the data files for |
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| 53 | DOLLOP. |
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| 54 | <P> |
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| 55 | The user interaction starts with the program presenting a menu. The |
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| 56 | menu looks like this: |
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| 57 | <P> |
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| 58 | <TABLE><TR><TD BGCOLOR=white> |
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| 59 | <PRE> |
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| 60 | |
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| 61 | Interactive Dollo or polymorphism parsimony, version 3.6a3 |
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| 62 | |
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| 63 | Settings for this run: |
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| 64 | P Parsimony method? Dollo |
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| 65 | A Use ancestral states? No |
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| 66 | F Use factors information? No |
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| 67 | W Sites weighted? No |
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| 68 | T Use Threshold parsimony? No, use ordinary parsimony |
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| 69 | A Use ancestral states in input file? No |
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| 70 | U Initial tree (arbitrary, user, specify)? Arbitrary |
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| 71 | 0 Graphics type (IBM PC, ANSI, none)? (none) |
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| 72 | L Number of lines on screen? 24 |
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| 73 | S Width of terminal screen? 80 |
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| 74 | |
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| 75 | |
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| 76 | Are these settings correct? (type Y or the letter for one to change) |
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| 77 | </PRE> |
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| 78 | </TD></TR></TABLE> |
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| 79 | <P> |
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| 80 | The P (Parsimony Method) option is the one that toggles between polymorphism |
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| 81 | parsimony and Dollo parsimony. The program defaults to Dollo parsimony. |
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| 82 | <P> |
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| 83 | The T (Threshold), F (Factors), A (Ancestors), and 0 (Graphics type) options |
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| 84 | are the usual |
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| 85 | ones and are described in the main documentation page and in the |
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| 86 | Discrete Characters Program documentation page. |
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| 87 | (<B>Note: at present DOLMOVE actully |
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| 88 | does not use the A (Ancestral states) information</B>). The F (Factors) |
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| 89 | option is used to inform the program which |
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| 90 | groups of characters are to be counted together in computing the number of |
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| 91 | characters compatible with the tree. Thus if three binary characters are all |
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| 92 | factors of the same multistate character, the multistate character will |
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| 93 | be counted as compatible with the tree only if all three factors are compatible |
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| 94 | with it. |
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| 95 | <P> |
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| 96 | The L option allows |
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| 97 | the program to take advantage of larger screens if available. The X (Mixed |
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| 98 | Methods option is not available in DOLMOVE. The |
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| 99 | U (initial tree) option allows the user to choose whether |
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| 100 | the initial tree is to be arbitrary, interactively specified by the user, or |
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| 101 | read from a tree file. Typing U causes the program to change among the |
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| 102 | three possibilities in turn. I |
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| 103 | would recommend that for a first run, you allow the tree to be set up |
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| 104 | arbitrarily (the default), as the "specify" choice is difficult |
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| 105 | to use and the "user tree" choice requires that you have available a tree file |
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| 106 | with the tree topology of the initial tree. |
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| 107 | Its default name is <TT>intree</TT>. The program will ask you for its name if |
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| 108 | it looks for the input tree file and does not find one of this name. |
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| 109 | If you wish to set up some |
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| 110 | particular tree you can also do that by the rearrangement commands specified |
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| 111 | below. The T (threshold) option allows a continuum of methods between |
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| 112 | parsimony and compatibility. Thresholds less than or equal to 0 do not |
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| 113 | have any |
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| 114 | meaning and should not be used: they will result in a tree dependent only on |
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| 115 | the input order of species and not at all on the data! |
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| 116 | Note that the usual W (Weights) option is not available in MOVE. We |
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| 117 | hope to add it soon. |
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| 118 | <P> |
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| 119 | After the initial menu is displayed and the choices are made, |
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| 120 | the program then sets up an initial tree and displays it. Below it will be a |
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| 121 | one-line menu of possible commands, which looks like this: |
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| 122 | <P> |
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| 123 | <PRE> |
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| 124 | NEXT? (Options: R # + - S . T U W O F C H ? X Q) (H or ? for Help) |
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| 125 | </PRE> |
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| 126 | <P> |
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| 127 | If you type H or ? you will get a single screen showing a description of each |
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| 128 | of these commands in a few words. Here are slightly more detailed |
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| 129 | descriptions: |
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| 130 | <P> |
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| 131 | <DL> |
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| 132 | <DT>R</DT> <DD>("Rearrange"). This command asks for the number of a node which is to be |
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| 133 | removed from the tree. It and everything to the right of it on the tree is to |
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| 134 | be removed (by breaking the branch immediately below it). The command also |
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| 135 | asks for the number of a node below which that group is to be inserted. If an |
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| 136 | impossible number is given, the program refuses to carry out the rearrangement |
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| 137 | and asks for a new command. The rearranged tree is displayed: it will often |
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| 138 | have a different number of steps than the original. If you wish to undo a |
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| 139 | rearrangement, use the Undo command, for which see below.</DD> |
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| 140 | <P> |
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| 141 | <DT>#</DT> <DD>This command, and the +, - and S commands described below, determine |
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| 142 | which character has its states displayed on the branches of |
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| 143 | the trees. The initial tree displayed by the program does not show |
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| 144 | states of sites. When # is typed, the program does not ask the user which |
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| 145 | character is to be shown but automatically shows the states of the next |
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| 146 | binary character that is not compatible with the tree (the next character that |
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| 147 | does not |
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| 148 | perfectly fit the current tree). The search for this character "wraps around" |
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| 149 | so that if it reaches the last character without finding one that is not |
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| 150 | compatible with the tree, the search continues at the first character; if no |
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| 151 | incompatible character is found the current character is shown, and if no |
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| 152 | current character is shown then the first character is shown. If the last |
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| 153 | character has been reached, using + again causes the first |
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| 154 | character to be shown. The display takes the form of |
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| 155 | different symbols or textures on the branches of the tree. The state of each |
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| 156 | branch is actually the state of the node above it. A key of the symbols or |
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| 157 | shadings used for states 0, 1 and ? are shown next to the tree. State ? means |
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| 158 | that either state 0 or state 1 could exist at that point on the tree, and that |
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| 159 | the user may want to consider the different possibilities, which are usually |
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| 160 | apparent by inspection. </DD> |
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| 161 | <DT>+</DT> <DD>This command is the same as # except that it goes forward one character, |
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| 162 | showing the states of the next character. If no character has been shown, |
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| 163 | using + will |
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| 164 | cause the first character to be shown. Once the last character has been |
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| 165 | reached, using + again will show the first character.</DD> |
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| 166 | <P> |
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| 167 | <DT>-</DT> <DD>This command is the same as + except that it goes backwards, showing the |
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| 168 | states of the previous character. If no character has been shown, using - will |
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| 169 | cause the last character to be shown. Once character number 1 has been |
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| 170 | reached, using - again will show the last character.</DD> |
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| 171 | <P> |
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| 172 | <DT>S</DT> <DD>("Show"). This command is the same as + and - except that it causes |
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| 173 | the program to ask you for the number of a character. That character is |
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| 174 | the one whose states will be displayed. If you give the character number as 0, |
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| 175 | the program will go back to not showing the states of the characters.</DD> |
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| 176 | <P> |
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| 177 | <DT>. (dot)</DT> <DD>This command simply causes the current tree to be redisplayed. It is of |
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| 178 | use when the tree has partly disappeared off of the top of the screen owing to |
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| 179 | too many responses to commands being printed out at the bottom of the screen. </DD> |
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| 180 | <P> |
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| 181 | <DT>T</DT> <DD>("Try rearrangements"). This command asks for the name of a node. The |
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| 182 | part of the tree at and above that node is removed from the tree. The program |
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| 183 | tries to re-insert it in each possible location on the tree (this may take some |
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| 184 | time, and the program reminds you to wait). Then it prints out a summary. For |
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| 185 | each possible location the program prints out the number of the node to the |
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| 186 | right of the |
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| 187 | place of insertion and the number of steps required in each case. These are |
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| 188 | divided into those that are better, tied, or worse than the current tree. Once |
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| 189 | this summary is printed out, the group that was removed is inserted into its |
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| 190 | original position. It is up to you to use the R command to actually carry out |
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| 191 | any the arrangements that have been tried. </DD> |
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| 192 | <P> |
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| 193 | <DT>U</DT> <DD>("Undo"). This command reverses the effect of the most recent |
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| 194 | rearrangement, outgroup re-rooting, or flipping of branches. It returns to the |
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| 195 | previous tree topology. It will be of great use when rearranging the tree and |
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| 196 | when a rearrangement proves worse than the preceding one -- it permits you to |
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| 197 | abandon the new one and return to the previous one without remembering its |
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| 198 | topology in detail.</DD> |
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| 199 | <P> |
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| 200 | <DT>W</DT> <DD>("Write"). This command writes out the current tree onto a tree output |
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| 201 | file. If the file already has been written to by this run of DOLMOVE, it will |
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| 202 | ask you whether you want to replace the contents of the file, add the tree to |
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| 203 | the end of the file, or not write out the tree to the file. The tree |
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| 204 | is written in the standard format used by PHYLIP (a subset of the |
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| 205 | Newick standard). It is in the proper format to serve as the |
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| 206 | User-Defined Tree for setting up the initial tree in a subsequent run of the |
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| 207 | program.</DD> |
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| 208 | <P> |
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| 209 | <DT>O</DT> <DD>("Outgroup"). This asks for the number of a node which is to be the |
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| 210 | outgroup. The tree will be redisplayed with that node |
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| 211 | as the left descendant of the bottom fork. The number of |
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| 212 | steps required on the tree may change on re-rooting. Note that it is possible |
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| 213 | to use this to make a multi-species group the outgroup (i.e., you can give the |
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| 214 | number of an interior node of the tree as the outgroup, and the program will |
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| 215 | re-root the tree properly with that on the left of the bottom fork).</DD> |
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| 216 | <P> |
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| 217 | <DT>F</DT> <DD>("Flip"). This asks for a node number and then flips the two branches at |
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| 218 | that, so that the left-right order of branches at that node is |
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| 219 | changed. This does not actually change the tree topology (or the number of |
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| 220 | steps on that tree) but it does change the appearance of the tree.</DD> |
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| 221 | <P> |
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| 222 | <DT>C</DT> <DD>("Clade"). When the data consist of more than 12 species (or more than |
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| 223 | half the number of lines on the screen if this is not 24), it may be |
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| 224 | difficult to display the tree on one screen. In that case the tree |
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| 225 | will be squeezed down to |
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| 226 | one line per species. This is too small to see all the interior states of the |
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| 227 | tree. The C command instructs the program to print out only that part of the |
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| 228 | tree (the "clade") from a certain node on up. The program will prompt you for |
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| 229 | the number of this node. Remember that thereafter you are not looking at the |
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| 230 | whole tree. To go back to looking at the whole tree give the C command again |
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| 231 | and enter "0" for the node number when asked. Most users will not want to use |
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| 232 | this option unless forced to.</DD> |
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| 233 | <P> |
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| 234 | <DT>H</DT> <DD>("Help"). Prints a one-screen summary of what the commands do, a few |
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| 235 | words for each command.</DD> |
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| 236 | <P> |
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| 237 | <DT>?</DT> <DD>("huh?"). A synonym for H. Same as Help command.</DD> |
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| 238 | <P> |
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| 239 | <DT>X</DT> <DD>("Exit"). Exit from program. If the current tree has not yet been saved |
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| 240 | into a file, the program will ask you whether it should be saved.</DD> |
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| 241 | <P> |
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| 242 | <DT>Q</DT> <DD>("Quit"). A synonym for X. Same as the eXit command.</DD> |
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| 243 | </DL> |
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| 244 | <P> |
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| 245 | <H2>OUTPUT</H2> |
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| 246 | <P> |
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| 247 | If the A option is used, then |
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| 248 | the program will infer, for any character whose ancestral state is unknown |
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| 249 | ("?") whether the ancestral state 0 or 1 will give the fewest changes |
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| 250 | (according to the criterion in use). If these are tied, then it may not be |
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| 251 | possible for the program to infer the state in the internal nodes, and many of |
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| 252 | these will be shown as "?". If the A option is not used, then the program will |
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| 253 | assume 0 as the ancestral state. |
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| 254 | <P> |
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| 255 | When reconstructing the placement of forward |
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| 256 | changes and reversions under the Dollo method, keep in mind that each |
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| 257 | polymorphic state in the input data will require one "last minute" |
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| 258 | reversion. This is included in the counts. Thus if we have both states 0 and |
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| 259 | 1 at a tip of the tree the program will assume that the lineage had state 1 up |
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| 260 | to the last minute, and then state 0 arose in that population by reversion, |
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| 261 | without loss of state 1. |
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| 262 | <P> |
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| 263 | When DOLMOVE calculates the number of characters |
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| 264 | compatible with the tree, it will take the F option into |
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| 265 | account and count the multistate characters as units, counting a character |
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| 266 | as compatible with the tree only when all of the binary characters |
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| 267 | corresponding to it are compatible with the tree. |
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| 268 | <P> |
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| 269 | <H2>ADAPTING THE PROGRAM TO YOUR COMPUTER AND TO YOUR TERMINAL</H2> |
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| 270 | <P> |
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| 271 | As we have seen, the initial menu of the program allows you to choose |
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| 272 | among three screen types (PC, ANSI, and none). |
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| 273 | If you want to |
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| 274 | avoid having to make this choice every time, you can change |
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| 275 | some of the |
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| 276 | constants in the file <TT>phylip.h</TT> to have the terminal type initialize |
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| 277 | itself in the proper way, and recompile. |
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| 278 | The constants that need attention are ANSICRT and IBMCRT. |
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| 279 | Currently these are both set to "false" on Macintosh and on Unix/Linux |
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| 280 | systems, and IBMCRT is set to "true" on Windows systems. If your system |
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| 281 | has an ANSI compatible terminal, you might want to find the |
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| 282 | definition of ANSICRT in <TT>phylip.h</TT> and set it to "true", and |
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| 283 | IBMCRT to "false". |
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| 284 | <P> |
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| 285 | <H2>MORE ABOUT THE PARSIMONY CRITERION</H2> |
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| 286 | <P> |
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| 287 | DOLMOVE uses as its numerical criterion the Dollo and |
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| 288 | polymorphism parsimony methods. The program defaults to carrying out Dollo |
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| 289 | parsimony. |
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| 290 | <P> |
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| 291 | The Dollo parsimony method was |
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| 292 | first suggested in print in verbal form by Le Quesne (1974) and was |
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| 293 | first well-specified by Farris (1977). The method is named after Louis |
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| 294 | Dollo since he was one of the first to assert that in evolution it is |
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| 295 | harder to gain a complex feature than to lose it. The algorithm |
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| 296 | explains the presence of the state 1 by allowing up to one forward |
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| 297 | change 0-->1 and as many reversions 1-->0 as are necessary to explain |
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| 298 | the pattern of states seen. The program attempts to minimize the number |
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| 299 | of 1-->0 reversions necessary. |
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| 300 | <P> |
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| 301 | The assumptions of this method are in effect: |
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| 302 | <P> |
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| 303 | <OL> |
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| 304 | <LI>We know which state is the ancestral one (state 0). |
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| 305 | <LI>The characters are evolving independently. |
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| 306 | <LI>Different lineages evolve independently. |
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| 307 | <LI>The probability of a forward change (0-->1) is small over the |
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| 308 | evolutionary times involved. |
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| 309 | <LI>The probability of a reversion (1-->0) is also small, but |
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| 310 | still far larger than the probability of a forward change, so |
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| 311 | that many reversions are easier to envisage than even one |
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| 312 | extra forward change. |
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| 313 | <LI>Retention of polymorphism for both states (0 and 1) is highly |
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| 314 | improbable. |
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| 315 | <LI>The lengths of the segments of the true tree are not so |
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| 316 | unequal that two changes in a long segment are as probable as |
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| 317 | one in a short segment. |
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| 318 | </OL> |
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| 319 | <P> |
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| 320 | One problem can arise when using additive binary recoding to |
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| 321 | represent a multistate character as a series of two-state characters. Unlike |
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| 322 | the Camin-Sokal, Wagner, and Polymorphism methods, the Dollo |
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| 323 | method can reconstruct ancestral states which do not exist. An example |
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| 324 | is given in my 1979 paper. It will be necessary to check the output to |
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| 325 | make sure that this has not occurred. |
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| 326 | <P> |
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| 327 | The polymorphism parsimony method was first used by me, |
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| 328 | and the results published |
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| 329 | (without a clear |
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| 330 | specification of the method) by Inger (1967). The method was |
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| 331 | published by Farris (1978a) and by me (1979). The method |
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| 332 | assumes that we can explain the pattern of states by no more than one |
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| 333 | origination (0-->1) of state 1, followed by retention of polymorphism |
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| 334 | along as many segments of the tree as are necessary, followed by loss of |
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| 335 | state 0 or of state 1 where necessary. The program tries to minimize |
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| 336 | the total number of polymorphic characters, where each polymorphism is |
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| 337 | counted once for each segment of the tree in which it is retained. |
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| 338 | <P> |
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| 339 | The assumptions of the polymorphism parsimony method are in effect: |
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| 340 | <P> |
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| 341 | <OL> |
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| 342 | <LI>The ancestral state (state 0) is known in each character. |
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| 343 | <LI>The characters are evolving independently of each other. |
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| 344 | <LI>Different lineages are evolving independently. |
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| 345 | <LI>Forward change (0-->1) is highly improbable over the length of |
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| 346 | time involved in the evolution of the group. |
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| 347 | <LI>Retention of polymorphism is also improbable, but far more |
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| 348 | probable that forward change, so that we can more easily |
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| 349 | envisage much polymorhism than even one additional forward |
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| 350 | change. |
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| 351 | <LI>Once state 1 is reached, reoccurrence of state 0 is very |
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| 352 | improbable, much less probable than multiple retentions of |
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| 353 | polymorphism. |
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| 354 | <LI>The lengths of segments in the true tree are not so unequal |
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| 355 | that we can more easily envisage retention events occurring in |
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| 356 | both of two long segments than one retention in a short |
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| 357 | segment. |
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| 358 | </OL> |
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| 359 | <P> |
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| 360 | That these are the assumptions of parsimony methods has been documented |
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| 361 | in a series of papers of mine: (1973a, 1978b, 1979, 1981b, |
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| 362 | 1983b, 1988b). For an opposing view arguing that the parsimony methods |
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| 363 | make no substantive |
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| 364 | assumptions such as these, see the papers by Farris (1983) and Sober (1983a, |
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| 365 | 1983b), but also read the exchange between Felsenstein and Sober (1986). |
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| 366 | <P> |
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| 367 | Below is a test data set, but we cannot show the |
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| 368 | output it generates because of the interactive nature of the program. |
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| 369 | <P> |
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| 370 | <HR> |
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| 371 | <P> |
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| 372 | <H3>TEST DATA SET</H3> |
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| 373 | <P> |
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| 374 | <TABLE><TR><TD BGCOLOR=white> |
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| 375 | <PRE> |
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| 376 | 5 6 |
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| 377 | Alpha 110110 |
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| 378 | Beta 110000 |
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| 379 | Gamma 100110 |
|---|
| 380 | Delta 001001 |
|---|
| 381 | Epsilon 001110 |
|---|
| 382 | </PRE> |
|---|
| 383 | </TD></TR></TABLE> |
|---|
| 384 | </BODY> |
|---|
| 385 | </HTML> |
|---|
