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| 11 | <BODY BGCOLOR="#ccffff"> |
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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>DNAMOVE - Interactive DNA parsimony</H1> |
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| 18 | </DIV> |
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| 19 | <P> |
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| 20 | © Copyright 1986-2002 by the University of |
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| 21 | Washington. Written by Joseph Felsenstein. Permission is granted to copy |
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| 22 | this document provided that no fee is charged for it and that this copyright |
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| 23 | notice is not removed. |
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| 24 | <P> |
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| 25 | DNAMOVE is an interactive DNA parsimony program, inspired by Wayne Maddison and |
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| 26 | David and Wayne Maddison's marvellous program MacClade, which is written for |
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| 27 | Macintosh computers. DNAMOVE reads in a data set which is prepared in almost |
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| 28 | the same format as one for the DNA parsimony program DNAPARS. It allows |
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| 29 | the user to choose an initial tree, and displays this tree on the screen. The |
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| 30 | user can look at different sites and the way the nucleotide states are |
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| 31 | distributed on that tree, given the most parsimonious reconstruction of state |
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| 32 | changes for that particular tree. The user then can specify how the tree is to |
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| 33 | be rearraranged, rerooted or written out to a file. By looking at different |
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| 34 | rearrangements of the tree the user can manually search for the most |
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| 35 | parsimonious tree, and can get a feel for how different sites are affected |
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| 36 | by changes in the tree topology. |
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| 37 | <P> |
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| 38 | This program uses graphic characters that show the tree to best |
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| 39 | advantage on some computer systems. |
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| 40 | Its graphic characters will work best on MSDOS systems or MSDOS windows in |
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| 41 | Windows, and to |
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| 42 | any system whose screen or terminals emulate ANSI standard terminals |
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| 43 | such as old Digital VT100 terminals, |
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| 44 | Telnet programs, |
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| 45 | or VT100-compatible windows in the X windowing system. |
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| 46 | For any other screen types, (such as Macintosh windows) there is a generic |
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| 47 | option which does |
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| 48 | not make use of screen graphics characters. The program will work well |
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| 49 | in those cases, but the tree it displays will look a bit uglier. |
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| 50 | <P> |
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| 51 | The input data file is set up almost identically to the data files for |
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| 52 | DNAPARS. The code for nucleotide sequences is the standard one, as |
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| 53 | described in the molecular sequence programs document. |
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| 54 | The user trees are contained in the input tree file |
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| 55 | which is used for input of the starting tree (if desired). The |
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| 56 | output tree file is used for the final tree. |
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| 57 | <P> |
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| 58 | The user interaction starts with the program presenting a menu. The |
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| 59 | menu looks like this: |
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| 60 | <P> |
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| 61 | <TABLE><TR><TD BGCOLOR=white> |
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| 62 | <PRE> |
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| 63 | |
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| 64 | Interactive DNA parsimony, version 3.6a3 |
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| 65 | |
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| 66 | Settings for this run: |
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| 67 | O Outgroup root? No, use as outgroup species 1 |
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| 68 | W Sites weighted? No |
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| 69 | T Use Threshold parsimony? No, use ordinary parsimony |
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| 70 | I Input sequences interleaved? Yes |
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| 71 | U Initial tree (arbitrary, user, specify)? Arbitrary |
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| 72 | 0 Graphics type (IBM PC, ANSI, none)? (none) |
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| 73 | S Width of terminal screen? 80 |
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| 74 | L Number of lines on screen? 24 |
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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 | |
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| 78 | </PRE> |
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| 79 | </TD></TR></TABLE> |
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| 80 | <P> |
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| 81 | The O (Outgroup), W (Weights), T (Threshold), and 0 (Graphics type) options |
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| 82 | are the usual |
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| 83 | ones and are described in the main documentation file. The I |
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| 84 | (Interleaved) option is the usual one and is described in the main |
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| 85 | documentation file and the molecular sequences programs documentation file. |
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| 86 | The U (initial tree) option allows the user to choose whether |
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| 87 | the initial tree is to be arbitrary, interactively specified by the user, or |
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| 88 | read from a tree file. Typing U causes the program to change among the |
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| 89 | three possibilities in turn. I |
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| 90 | would recommend that for a first run, you allow the tree to be set up |
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| 91 | arbitrarily (the default), as the "specify" choice is difficult |
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| 92 | to use and the "user tree" choice requires that you have available a tree file |
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| 93 | with the tree topology of the initial tree, which must be a rooted tree. |
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| 94 | Its default name is <TT>intree</TT>. The program will ask you for its name if |
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| 95 | it looks for the input tree file and does not find one of this name. |
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| 96 | If you wish to set up some |
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| 97 | particular tree you can also do that by the rearrangement commands specified |
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| 98 | below. |
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| 99 | <P> |
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| 100 | The W (Weights) option allows only weights of 0 or 1. |
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| 101 | <P> |
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| 102 | The T (threshold) option allows a continuum of methods between parsimony and |
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| 103 | compatibility. Thresholds less than or equal to 1.0 do not have any |
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| 104 | meaning and should not be used: they will result in a tree dependent only on |
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| 105 | the input order of species and not at all on the data! |
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| 106 | <P> |
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| 107 | The L (screen Lines) option allows the user to change the height of the |
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| 108 | screen (in lines of characters) that is assumed to be available on the |
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| 109 | display. This may be particularly helpful when displaying large trees |
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| 110 | on terminals that have more than 24 lines per screen, or on workstation |
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| 111 | or X-terminal screens that can emulate the ANSI terminals with more than |
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| 112 | 24 lines. |
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| 113 | <P> |
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| 114 | After the initial menu is displayed and the choices are made, |
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| 115 | the program then sets up an initial tree and displays it. Below it will be a |
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| 116 | one-line menu of possible commands, which looks like this: |
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| 117 | <P> |
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| 118 | <PRE> |
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| 119 | NEXT? (Options: R # + - S . T U W O F C H ? X Q) (H or ? for Help) |
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| 120 | </PRE> |
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| 121 | <P> |
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| 122 | If you type H or ? you will get a single screen showing a description of each |
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| 123 | of these commands in a few words. Here are slightly more detailed |
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| 124 | descriptions: |
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| 125 | <P> |
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| 126 | <DL> |
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| 127 | <DT>R ("Rearrange")</DT> <DD> This command asks for the number of a node which is to be |
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| 128 | removed from the tree. It and everything to the right of it on the tree is to |
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| 129 | be removed (by breaking the branch immediately below it). The command also |
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| 130 | asks for the number of a node below which that group is to be inserted. If an |
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| 131 | impossible number is given, the program refuses to carry out the rearrangement |
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| 132 | and asks for a new command. The rearranged tree is displayed: it will often |
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| 133 | have a different number of steps than the original. If you wish to undo a |
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| 134 | rearrangement, use the Undo command, for which see below.</DD> |
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| 135 | <DT>#</DT> <DD>This command, and the +, - and S commands described below, determine |
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| 136 | which site has its states displayed on the branches of |
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| 137 | the trees. The initial tree displayed by the program does not show |
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| 138 | states of sites. When # is typed, the program does not ask the user which |
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| 139 | site is to be shown but automatically shows the states of the next |
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| 140 | site that is not compatible with the tree (the next site that does not |
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| 141 | perfectly fit the current tree). The search for this site "wraps around" |
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| 142 | so that if it reaches the last site without finding one that is not |
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| 143 | compatible with the tree, the search continues at the first site; if no |
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| 144 | incompatible site is found the current site is shown again, and if no current |
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| 145 | site is being shown then the first site is shown. The display takes the form of |
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| 146 | different symbols or textures on the branches of the tree. The state of each |
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| 147 | branch is actually the state of the node above it. A key of the symbols or |
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| 148 | shadings used for states A, C, G, T (U) and ? are shown next to the |
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| 149 | tree. State ? means that more than one possible nucleotide could exist at |
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| 150 | that point |
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| 151 | on the tree, and that the user may want to consider the different |
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| 152 | possibilities, which are usually apparent by inspection.</DD> |
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| 153 | <DT>+</DT> <DD>This command is the same as \# except that it goes forward one site, |
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| 154 | showing the states of the next site. If no site has been shown, using + will |
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| 155 | cause the first site to be shown. Once the last site has been |
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| 156 | reached, using + again will show the first site.</DT> |
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| 157 | <P> |
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| 158 | <DT>-</DT> <DD>This command is the same as + except that it goes backwards, showing the |
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| 159 | states of the previous site. If no site has been shown, using - will |
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| 160 | cause the last site to be shown. Once site number 1 has been |
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| 161 | reached, using - again will show the last site.</DD> |
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| 162 | <DT>S ("Show").</DT> <DD> This command is the same as + and - except that it causes |
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| 163 | the program to ask you for the number of a site. That site is |
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| 164 | the one whose states will be displayed. If you give the site number as 0, |
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| 165 | the program will go back to not showing the states of the sites.</DD> |
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| 166 | <DT>. (dot)</DT> <DD>This command simply causes the current tree to be redisplayed. It is of |
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| 167 | use when the tree has partly disappeared off of the top of the screen owing to |
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| 168 | too many responses to commands being printed out at the bottom of the screen. |
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| 169 | </DD> |
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| 170 | <P> |
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| 171 | <DT>T ("Try rearrangements").</DT> <DD>This command asks for the name of a node. The |
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| 172 | part of the tree at and above that node is removed from the tree. The program |
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| 173 | tries to re-insert it in each possible location on the tree (this may take some |
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| 174 | time, and the program reminds you to wait). Then it prints out a summary. For |
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| 175 | each possible location the program prints out the number of the node to the |
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| 176 | right of the |
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| 177 | place of insertion and the number of steps required in each case. These are |
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| 178 | divided into those that are better then or tied with the current tree. Once |
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| 179 | this summary is printed out, the group that was removed is reinserted into its |
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| 180 | original position. It is up to you to use the R command to actually carry out |
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| 181 | any of the arrangements that have been tried. </DD> |
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| 182 | <DT>U ("Undo").</DT> <DD>This command reverses the effect of the most recent |
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| 183 | rearrangement, outgroup re-rooting, or flipping of branches. It returns to the |
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| 184 | previous tree topology. It will be of great use when rearranging the tree and |
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| 185 | when a rearrangement proves worse than the preceding one -- it permits you to |
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| 186 | abandon the new one and return to the previous one without remembering its |
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| 187 | topology in detail.</DD> |
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| 188 | <DT>W ("Write").</DT> <DD>This command writes out the current tree onto a tree output |
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| 189 | file. If the file already has been written to by this run of DNAMOVE, it will |
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| 190 | ask you whether you want to replace the contents of the file, add the tree to |
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| 191 | the end of the file, or not write out the tree to the file. The tree |
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| 192 | is written in the standard format used by PHYLIP (a subset of the |
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| 193 | Newick standard). It is in the proper format to serve as the |
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| 194 | User-Defined Tree for setting up the initial tree in a subsequent run of the |
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| 195 | program. Note that if you provided the initial tree topology in a tree file |
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| 196 | and replace its contents, that initial tree will be lost.</DD> |
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| 197 | <DT>O ("Outgroup").</DT> <DD>This asks for the number of a node which is to be the |
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| 198 | outgroup. The tree will be redisplayed with that node |
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| 199 | as the left descendant of the bottom fork. Note that it is possible to |
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| 200 | use this to make a multi-species group the outgroup (i.e., you can give the |
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| 201 | number of an interior node of the tree as the outgroup, and the program will |
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| 202 | re-root the tree properly with that on the left of the bottom fork.</DD> |
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| 203 | <DT>F ("Flip").</DT> <DD>This asks for a node number and then flips the two branches at |
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| 204 | that node, so that the left-right order of branches at that node is |
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| 205 | changed. This does not actually change the tree topology (or the number of |
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| 206 | steps on that tree) but it does change the appearance of the tree.</DD> |
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| 207 | <DT>C ("Clade").</DT> <DD>When the data consist of more than 12 species (or more than |
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| 208 | half the number of lines on the screen if this is not 24), it may be |
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| 209 | difficult to display the tree on one screen. In that case the tree |
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| 210 | will be squeezed down to |
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| 211 | one line per species. This is too small to see all the interior states of the |
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| 212 | tree. The C command instructs the program to print out only that part of the |
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| 213 | tree (the "clade") from a certain node on up. The program will prompt you for |
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| 214 | the number of this node. Remember that thereafter you are not looking at the |
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| 215 | whole tree. To go back to looking at the whole tree give the C command again |
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| 216 | and enter "0" for the node number when asked. Most users will not want to use |
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| 217 | this option unless forced to.</DD> |
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| 218 | <DT>H ("Help").</DT> <DD>Prints a one-screen summary of what the commands do, a few |
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| 219 | words for each command.</DD> |
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| 220 | <DT>? ("huh?").</DT> <DD>A synonym for H. Same as Help command.</DD> |
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| 221 | <DT>X ("Exit").</DT> <DD>Exit from program. If the current tree has not yet been saved |
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| 222 | into a file, the program will first ask you whether it should be saved.</DD> |
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| 223 | <DT>Q ("Quit").</DT> <DD>A synonym for X. Same as the eXit command.</DD> |
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| 224 | </DL> |
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| 225 | <P> |
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| 226 | <H3>ADAPTING THE PROGRAM TO YOUR COMPUTER AND TO YOUR TERMINAL</H3> |
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| 227 | <P> |
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| 228 | As we have seen, the initial menu of the program allows you to choose |
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| 229 | among three screen types (PCDOS, Ansi, and none). We have tried to |
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| 230 | have the default values be correct for PC, Macintosh, and Unix |
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| 231 | screens. If the setting is "none" (which is necessary on |
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| 232 | Macintosh screens), the special graphics |
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| 233 | characters will not be used to indicate nucleotide states, but only letters |
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| 234 | will be used for the four nucleotides. This is less easy to look at. |
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| 235 | <P> |
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| 236 | <H2>MORE ABOUT THE PARSIMONY CRITERION</H2> |
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| 237 | <P> |
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| 238 | This program carries out unrooted parsimony (analogous to Wagner |
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| 239 | trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA |
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| 240 | sequences. The method of Fitch (1971) is used to count the number of |
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| 241 | changes of base needed on a given tree. The assumptions of this |
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| 242 | method are exactly analogous to those of MIX: |
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| 243 | <P> |
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| 244 | <OL> |
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| 245 | <LI>Each site evolves independently. |
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| 246 | <LI>Different lineages evolve independently. |
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| 247 | <LI>The probability of a base substitution at a given site is |
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| 248 | small over the lengths of time involved in |
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| 249 | a branch of the phylogeny. |
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| 250 | <LI>The expected amounts of change in different branches of the phylogeny |
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| 251 | do not vary by so much that two changes in a high-rate branch |
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| 252 | are more probable than one change in a low-rate branch. |
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| 253 | <LI>The expected amounts of change do not vary enough among sites that two |
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| 254 | changes in one site are more probable than one change in another. |
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| 255 | </OL> |
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| 256 | <P> |
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| 257 | That these are the assumptions of parsimony methods has been documented |
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| 258 | in a series of papers of mine: (1973a, 1978b, 1979, 1981b, |
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| 259 | 1983b, 1988b). For an opposing view arguing that the parsimony methods |
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| 260 | make no substantive |
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| 261 | assumptions such as these, see the papers by Farris (1983) and Sober (1983a, |
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| 262 | 1983b), but also read the exchange between Felsenstein and Sober (1986). |
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| 263 | <P> |
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| 264 | Change from an occupied site to a deletion is counted as one |
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| 265 | change. Reversion from a deletion to an occupied site is allowed and is also |
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| 266 | counted as one change. |
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| 267 | <P> |
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| 268 | Below is a test data set, but we cannot show the |
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| 269 | output it generates because of the interactive nature of the program. |
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| 270 | <P> |
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| 271 | <HR> |
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| 272 | <P> |
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| 273 | <H3>DATA SET</H3> |
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| 274 | <P> |
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| 275 | <TABLE><TR><TD BGCOLOR=white> |
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| 276 | <PRE> |
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| 277 | 5 13 |
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| 278 | Alpha AACGUGGCCA AAU |
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| 279 | Beta AAGGUCGCCA AAC |
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| 280 | Gamma CAUUUCGUCA CAA |
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| 281 | Delta GGUAUUUCGG CCU |
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| 282 | Epsilon GGGAUCUCGG CCC |
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| 283 | </PRE> |
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| 284 | </TD></TR></TABLE> |
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| 285 | </BODY> |
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| 286 | </HTML> |
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