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| 4 | <TITLE>discrete</TITLE> |
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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>DOCUMENTATION FOR (0,1) DISCRETE CHARACTER PROGRAMS</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 | These programs are intended for the use of morphological |
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| 26 | systematists who are dealing with discrete characters, |
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| 27 | or by molecular evolutionists dealing with presence-absence data on |
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| 28 | restriction sites. One of the programs (PARS) allows multistate |
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| 29 | characters, with up to 8 states, plus the unknown state symbol "?". |
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| 30 | For the others, the characters |
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| 31 | are assumed to be coded into a series of (0,1) two-state characters. For |
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| 32 | most of the programs there are two other states possible, "P", which |
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| 33 | stands for the state of Polymorphism for both states (0 and 1), and "?", |
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| 34 | which stands for the state of ignorance: it is the state "unknown", or |
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| 35 | "does not apply". The state "P" can also be denoted by "B", for "both". |
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| 36 | <P> |
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| 37 | There is a method invented by Sokal and Sneath (1963) for linear |
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| 38 | sequences of character states, and fully developed for branching sequences |
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| 39 | of character states |
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| 40 | by Kluge and Farris (1969) for recoding a multistate character |
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| 41 | into a series of two-state (0,1) characters. Suppose we had a character |
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| 42 | with four states whose character-state tree had the rooted form: |
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| 43 | <P> |
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| 44 | <PRE> |
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| 45 | 1 ---> 0 ---> 2 |
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| 46 | | |
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| 47 | | |
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| 48 | V |
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| 49 | 3 |
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| 50 | </PRE> |
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| 51 | <P> |
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| 52 | <P> |
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| 53 | so that 1 is the ancestral state and 0, 2 and 3 derived states. We can |
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| 54 | represent this as three two-state characters: |
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| 55 | <P> |
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| 56 | <PRE> |
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| 57 | Old State New States |
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| 58 | --- ----- --- ------ |
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| 59 | 0 001 |
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| 60 | 1 000 |
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| 61 | 2 011 |
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| 62 | 3 101 |
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| 63 | </PRE> |
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| 64 | <P> |
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| 65 | The three new states correspond to the three arrows in the above character |
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| 66 | state tree. Possession of one of the new states corresponds to whether or not |
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| 67 | the old state had that arrow in its ancestry. Thus the first new state |
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| 68 | corresponds to the bottommost arrow, which only state 3 has in its ancestry, |
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| 69 | the second state to the rightmost of the top arrows, and the third state to |
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| 70 | the leftmost top arrow. This coding will guarantee that the number of times |
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| 71 | that states arise on the tree (in programs MIX, MOVE, PENNY and BOOT) |
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| 72 | or the number of polymorphic states in a tree segment (in the Polymorphism |
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| 73 | option of DOLLOP, DOLMOVE, DOLPENNY and DOLBOOT) will correctly |
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| 74 | correspond to what would have been the case had our programs been able to take |
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| 75 | multistate characters into account. Although I have shown the above character |
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| 76 | state tree as rooted, the recoding method works equally well on unrooted |
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| 77 | multistate characters as long as the connections between the states are known |
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| 78 | and contain no loops. |
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| 79 | <P> |
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| 80 | However, in the default option of programs DOLLOP, DOLMOVE, DOLPENNY |
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| 81 | and DOLBOOT the multistate recoding does not necessarily work properly, as it |
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| 82 | may lead the program to reconstruct nonexistent state combinations such as |
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| 83 | 010. An example of this problem is given in my paper on alternative |
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| 84 | phylogenetic methods (1979). |
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| 85 | <P> |
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| 86 | If you have multistate character data where the states are connected in a |
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| 87 | branching "character state tree" you may want to do the binary recoding |
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| 88 | yourself. Thanks to Christopher Meacham, the package contains |
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| 89 | a program, FACTOR, which will do the recoding itself. For details see |
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| 90 | the documentation file for FACTOR. |
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| 91 | <P> |
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| 92 | We now also have the program PARS, which can do parsimony for unordered |
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| 93 | character states. |
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| 94 | <P> |
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| 95 | <H2>COMPARISON OF METHODS</H2> |
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| 96 | <P> |
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| 97 | The methods used in these programs make different assumptions about |
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| 98 | evolutionary rates, probabilities of different kinds of events, and our |
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| 99 | knowledge about the characters or about the character state trees. |
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| 100 | Basic references on these assumptions are my 1979, 1981b and 1983b |
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| 101 | papers, particularly the latter. The |
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| 102 | assumptions of each method are briefly described in the documentation |
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| 103 | file for the corresponding program. In most cases my assertions about what are |
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| 104 | the assumptions of these methods are challenged by others, whose papers I also |
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| 105 | cite at that point. Personally, I believe that they are wrong and I am |
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| 106 | right. I must emphasize the importance of |
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| 107 | understanding the assumptions underlying the methods you are using. No |
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| 108 | matter how fancy the algorithms, how maximum the likelihood or how |
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| 109 | minimum the number of steps, your results can only be as good as the |
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| 110 | correspondence between biological reality and your assumptions! |
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| 111 | <P> |
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| 112 | <H2>INPUT FORMAT</H2> |
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| 113 | <P> |
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| 114 | The input format is as described in the general documentation file. The |
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| 115 | input starts with a line containing the number of |
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| 116 | species and the number of characters. |
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| 117 | <P> |
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| 118 | In PARS, each character can have up to 8 states plus a "?" state. In any |
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| 119 | character, the first 8 symbols encountered will be taken to represent |
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| 120 | these states. Any of the digits 0-9, letters A-Z and a-z, and even symbols |
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| 121 | such as + and -, can be used (and in fact which 8 symbols are used can |
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| 122 | be different in different characters). |
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| 123 | <P> |
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| 124 | In the other discrete characters programs the allowable states are, |
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| 125 | 0, 1, P, B, and ?. Blanks |
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| 126 | may be included between the states (i. e. you can have a |
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| 127 | species whose data is DISCOGLOSS0 1 1 0 1 1 1). It is possible for |
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| 128 | extraneous information to follow the end of the character state data on |
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| 129 | the same line. For example, if there were 7 characters in the data set, |
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| 130 | a line of species data could read "DISCOGLOSS0110111 Hello there"). |
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| 131 | <P> |
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| 132 | The discrete character data can continue to a new line whenever needed. |
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| 133 | The characters are not in the "aligned" or "interleaved" format used by the |
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| 134 | molecular sequence programs: they have the name and entire set of characters |
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| 135 | for one species, then the name and entire set of characters for the next |
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| 136 | one, and so on. This is known as the sequential format. Be particularly |
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| 137 | careful when you use restriction sites |
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| 138 | data, which can be in either the aligned or the sequential format for use in |
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| 139 | RESTML but must be in the sequential format for these discrete character |
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| 140 | programs. |
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| 141 | <P> |
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| 142 | For PARS the discrete character data can be in either Sequential or |
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| 143 | Interleaved format; the latter is the default. |
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| 144 | <P> |
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| 145 | Errors in the input data will often be detected by the programs, and this will |
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| 146 | cause them to issue an error message such as 'BAD OUTGROUP NUMBER: ' together |
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| 147 | with information as to which species, character, or in this case outgroup |
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| 148 | number is the incorrect one. The program will them terminate; you will have |
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| 149 | to look at the data and figure out what went wrong and fix it. Often an error |
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| 150 | in the data causes a lack of synchronization between what is in the data file |
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| 151 | and what the program thinks is to be there. Thus a missing character may |
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| 152 | cause the program to read part of the next species name as a character and |
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| 153 | complain about its value. In this type of case you should look for the error |
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| 154 | earlier in the data file than the point about which the program is |
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| 155 | complaining. |
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| 156 | <P> |
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| 157 | <H2>OPTIONS GENERALLY AVAILABLE</H2> |
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| 158 | <P> |
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| 159 | Specific information on options will be given in the documentation |
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| 160 | file associated with each program. However, some options occur in many |
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| 161 | programs. Options are selected from the menu in each |
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| 162 | program, but the Old Style programs CLIQUE and FACTOR require information to be put into |
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| 163 | the beginning of the input file (Particularly the Ancestors, Factors, Weights, |
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| 164 | and Mixtures options). The options information described here is for |
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| 165 | the other programs. See the documentation page for CLIQUE and |
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| 166 | FACTOR to find out how they get their options information. |
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| 167 | <P> |
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| 168 | <UL> |
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| 169 | <LI>The A (Ancestral states) option. This indicates that we are |
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| 170 | specifying the ancestral states for each character. In the menu the |
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| 171 | ancestors (A) option must be selected. |
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| 172 | An ancestral states input file is read, whose default name is |
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| 173 | <TT>ancestors</TT>. It contains |
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| 174 | a line or lines giving the ancestral states for each character. |
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| 175 | These may be 0, 1 or ?, the latter |
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| 176 | indicating that the ancestral state is unknown. |
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| 177 | <P> |
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| 178 | An example is: |
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| 179 | <P> |
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| 180 | 001??11 |
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| 181 | <P> |
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| 182 | The ancestor information can be continued to a new line and can have blanks |
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| 183 | between any of the characters in the same way that species character data |
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| 184 | can. |
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| 185 | In the program CLIQUE the ancestor is instead to be included as a |
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| 186 | regular species and |
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| 187 | no A option is available. |
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| 188 | <P> |
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| 189 | <LI>The F (Factors) option. This is used in programs MOVE, DOLMOVE, |
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| 190 | and FACTOR. It specifies which binary characters correspond |
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| 191 | to which multistate characters. To use the F option you |
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| 192 | choose the F option in the program menu. After that the program |
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| 193 | will read a factors file (default name <TT>factors</TT> |
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| 194 | Which consists of a line or lines containing a symbol |
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| 195 | for each binary character. The |
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| 196 | symbol can be anything, provided that it is the same for binary characters |
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| 197 | that correspond to the same multistate character, and changes between |
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| 198 | multistate characters. A good practice is to make it the lower-order digit |
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| 199 | of the number of the multistate character. |
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| 200 | <P> |
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| 201 | For example, if there were 20 binary characters that had been generated by |
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| 202 | nine multistate characters having respectively 4, 3, 3, 2, 1, 2, 2, 2, and 1 |
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| 203 | binary factors you would make the factors file be: |
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| 204 | <P> |
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| 205 | 11112223334456677889 |
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| 206 | <P> |
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| 207 | although it could equivalently be: |
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| 208 | <P> |
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| 209 | aaaabbbaaabbabbaabba |
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| 210 | <P> |
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| 211 | All that is important is that the symbol |
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| 212 | for each binary character change only when adjacent binary characters |
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| 213 | correspond to different mutlistate characters. The factors |
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| 214 | file contents |
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| 215 | can continue to a new line at any time except during the initial characters |
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| 216 | filling out the length of a species name. |
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| 217 | <P> |
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| 218 | In programs CLIQUE and FACTOR the factors information is given in |
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| 219 | the Old Style system of putting that information into the input |
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| 220 | data file. The method for doing so is described in the documentation |
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| 221 | files for these programs. We hope to change this in the next |
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| 222 | release to use an input factors file. |
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| 223 | <P> |
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| 224 | <LI>The J (Jumble) option. This causes the species to be entered into the |
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| 225 | tree in a random order rather than in their order in the input file. The |
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| 226 | program prompts you for a random number seed. This option is described in |
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| 227 | the main documentation file. |
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| 228 | <P> |
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| 229 | <LI>The M (Multiple data sets) option. This has also been described in the |
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| 230 | main documentation file. It is not to be confused with the M option specified |
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| 231 | in the input file, which is the Mixture of methods option (yes, I know |
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| 232 | this is confusing). |
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| 233 | <P> |
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| 234 | <LI>The O (outgroup) option. This has also already been discussed in the |
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| 235 | general documentation file. It specifies the number of the particular species |
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| 236 | which will be used as the outgroup in rerooting the final tree when it is |
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| 237 | printed out. It will not have any effect if the tree is already rooted or is |
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| 238 | a user-defined tree. This option is not available in DOLLOP, DOLMOVE, |
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| 239 | or DOLPENNY, which always infer a rooted tree, or CLIQUE, which |
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| 240 | requires you to work out the rerooting by hand. The menu selection will |
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| 241 | cause you to be prompted for the number of the outgroup. |
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| 242 | <P> |
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| 243 | <LI>The T (threshold) option. This sets a threshold such that if the |
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| 244 | number of steps counted in a character is higher than the threshold, it |
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| 245 | will be taken to be the threshold value rather than the actual number of |
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| 246 | steps. This option has already been described in the main documentation |
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| 247 | file. The user is prompted for the threshold value. My 1981 paper |
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| 248 | (Felsenstein, 1981b) |
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| 249 | explains the logic behind the Threshold option, which is an attarctive |
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| 250 | alternative to successive weighting of characters. |
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| 251 | <P> |
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| 252 | <LI>The U (User tree) option. This has already been described in the |
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| 253 | main documentation file. For all of these programs user trees are to be |
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| 254 | specified as bifurcating trees, even in the cases where the tree that |
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| 255 | is inferred by the programs is to be regarded as unrooted. |
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| 256 | <P> |
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| 257 | <LI>The W (Weights) option. This allows us to specify weights on the |
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| 258 | characters, including the possibility of omitting characters from the |
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| 259 | analysis. It has already been described in the main documentation file. If |
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| 260 | the Weights option is used there must be a W on the first line of the |
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| 261 | input file. |
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| 262 | <P> |
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| 263 | <LI>The X (miXture) option. In the programs MIX, MOVE, and PENNY |
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| 264 | the user can specify for each character which parsimony method is |
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| 265 | in effect. This is done by selecting menu option X (not M) and having |
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| 266 | an input mixture file, whose default name is <TT>mixture</TT>. |
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| 267 | It contains a line or lines with and one letter for |
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| 268 | each character. These letters are C or S if the character is to |
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| 269 | be reconstructed according to Camin-Sokal parsimony, W or ? if the |
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| 270 | character is to be reconstructed according to Wagner parsimony. So if |
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| 271 | there are 20 characters the line giving the mixture might look like this: |
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| 272 | <P> |
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| 273 | <PRE> |
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| 274 | WWWCC WWCWC |
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| 275 | </PRE> |
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| 276 | <P> |
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| 277 | Note that blanks in the seqence of characters (after the first ones that |
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| 278 | are as long as the species names) will be ignored, and the information |
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| 279 | can go on to a new line at any point. So this could equally well have been |
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| 280 | specified by |
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| 281 | <P> |
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| 282 | <PRE> |
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| 283 | WW |
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| 284 | CCCWWCWC |
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| 285 | </PRE> |
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| 286 | </UL> |
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| 287 | <P> |
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| 288 | 30! 1 2 1 1 1 2 1 3 1 1 |
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| 289 | 40! 1 |
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| 290 | </PRE> |
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| 291 | <P> |
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| 292 | The numbers across the top and down the side indicate which character |
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| 293 | is being referred to. Thus character 23 is column "3" of row "20" |
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| 294 | and has 2 steps in this case. |
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| 295 | <P> |
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| 296 | I cannot emphasize too strongly that just because the tree diagram |
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| 297 | which the program prints out contains a particular |
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| 298 | branch DOES NOT MEAN |
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| 299 | THAT WE HAVE EVIDENCE THAT THE BRANCH IS OF NONZERO LENGTH. |
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| 300 | In program PARS the branches have lengths estimated and there |
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| 301 | can be trifurcations, but in all other discrete characters programs |
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| 302 | the procedure which prints out the tree cannot cope with a trifurcation, nor |
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| 303 | can the internal data structures used in my programs. Therefore, even |
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| 304 | when we have no resolution and a multifurcation, successive bifurcations |
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| 305 | will be printed out, although some of the branches shown will in fact |
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| 306 | actually be of zero length. To find out which, you will have to work out |
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| 307 | character by character where the placements of the changes on the tree |
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| 308 | are, under all possible ways that the changes can be placed on that |
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| 309 | tree. |
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| 310 | <P> |
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| 311 | In PARS the trees are truly multifurcating, and the search is over both |
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| 312 | bifurcating and multifurcating trees. A branch is retained in a tree only |
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| 313 | if there is at least one character, under at least one possible most |
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| 314 | parsimonious reconstruction of the placement of changes, that has a change in |
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| 315 | that branch. This means that two branches can both be present which are, |
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| 316 | however, not both in existence at the same time (in that there is no |
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| 317 | most parsimonious reconstruction of changes n the characters that has changes |
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| 318 | in both these branches at the same time). |
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| 319 | <P> |
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| 320 | In PARS, MIX, PENNY, DOLLOP, and DOLPENNY the trees will be (if the user selects |
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| 321 | the option to see them) |
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| 322 | accompanied by tables showing the reconstructed states of the characters in |
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| 323 | the hypothetical ancestral nodes in the interior of the tree. This will enable |
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| 324 | you to reconstruct where the changes were in each of the characters. In some |
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| 325 | cases the state shown in an interior node will be "?", which means that either |
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| 326 | 0 or 1 would be possible at that point. In such cases you have to work out |
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| 327 | the ambiguity by hand. A unique assignment of locations of changes is often |
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| 328 | not possible in the case of the Wagner parsimony method. There may be multiple |
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| 329 | ways of assigning changes to segments of the tree with that method. Printing |
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| 330 | only one would be misleading, as it might imply that certain segments of the |
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| 331 | tree had no change, when another equally valid assignment would put changes |
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| 332 | there. It must be emphasized that all these multiple assignments have exactly |
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| 333 | equal numbers of total changes, so that none is preferred over any other. |
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| 334 | <P> |
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| 335 | I have followed the convention of having |
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| 336 | a "." printed out in the table of character states of the hypothetical |
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| 337 | ancestral nodes whenever a state is 0 or 1 and its immediate ancestor is the |
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| 338 | same. This has the effect of highlighting the places where changes might have |
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| 339 | occurred and making it easy for the user to reconstruct all the alternative |
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| 340 | patterns of the characters states in the hypothetical ancestral nodes. |
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| 341 | In PARS you can, using the menu, turn off this dot-differencing |
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| 342 | convention and see all states at all hypothetical ancestral nodes of the tree. |
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| 343 | <P> |
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| 344 | On the line in that table corresponding to each branch of the tree will also |
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| 345 | be printed "yes", "no" or "maybe" as an answer to the question of whether this |
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| 346 | branch is of nonzero length. If there is no evidence that any character has |
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| 347 | changed in that branch, then "no" will be printed. If there is definite |
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| 348 | evidence that one has changed, then "yes" will be printed. If the matter is |
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| 349 | ambiguous, then "maybe" will be printed. You should keep in mind that all of |
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| 350 | these conclusions assume that we are only interested in the assignment of |
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| 351 | states that requires the least amount of change. In reality, the confidence |
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| 352 | limit on tree topology usually includes many different topologies, and |
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| 353 | presumably also then the confidence limits on amounts of change in branches |
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| 354 | are also very broad. |
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| 355 | <P> |
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| 356 | In addition to the table showing numbers of events, a table may be printed out |
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| 357 | showing which ancestral state causes the fewest events for each |
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| 358 | occurred and making it easy for the user to reconstruct all the alternative |
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| 359 | patterns of the characters states in the hypothetical ancestral nodes. |
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| 360 | In PARS you can, using the menu, turn off this dot-differencing |
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| 361 | convention and see all states at all hypothetical ancestral nodes of the tree. |
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| 362 | <P> |
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| 363 | On the line in that table corresponding to each branch of the tree will also |
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| 364 | be printed "yes", "no" or "maybe" as an answer to the question of whether this |
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| 365 | branch is of nonzero length. If there is no evidence that any character has |
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| 366 | changed in that branch, then "no" will be printed. If there is definite |
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| 367 | evidence that one has changed, then "yes" will be printed. If the matter is |
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| 368 | ambiguous, then "maybe" will be printed. You should keep in mind that all of |
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| 369 | these conclusions assume that we are only interested in the assignment of |
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| 370 | states that requires the least amount of change. In reality, the confidence |
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| 371 | limit on tree topology usually includes many different topologies, and |
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| 372 | presumably also then the confidence limits on amounts of change in branches |
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| 373 | are also very broad. |
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| 374 | <P> |
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| 375 | In addition to the table showing numbers of events, a table may be printed out |
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| 376 | showing which ancestral state causes the fewest events for each |
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| 377 | character. This will not always be done, but only when the tree is rooted and |
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| 378 | some ancestral states are unknown. This can be used to infer states of |
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| 379 | ancestors. For example, if you use the O (Outgroup) and A (Ancestral states) |
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| 380 | options together, with at least some of the ancestral states being given as |
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| 381 | "?", then inferences will be made for those characters, as the outgroup makes |
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| 382 | the tree rooted if it was not already. |
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| 383 | <P> |
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| 384 | In programs MIX and PENNY, if you are using the Camin-Sokal parsimony option |
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| 385 | with ancestral state "?" and it turns out that the program cannot decide |
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| 386 | between ancestral states 0 and 1, it will fail to even attempt reconstruction |
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| 387 | of states of the hypothetical ancestors, printing them all out as "." for |
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| 388 | those characters. This is done for internal bookkeeping reasons -- to |
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| 389 | reconstruct their changes would require a fair amount of additional code and |
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| 390 | additional data structures. It is not too hard to reconstruct the internal |
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| 391 | states by hand, trying the two possible ancestral states one after the |
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| 392 | other. A similar comment applies to the use of ancestral state "?" in the |
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| 393 | Dollo or Polymorphism parsimony methods (programs DOLLOP and DOLPENNY) which |
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| 394 | also can result in a similar hesitancy to print the estimate of the states of |
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| 395 | the hypothetical ancestors. In all of these cases the program will print "?" |
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| 396 | rather than "no" when it describes whether there are any changes in a branch, |
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| 397 | since there might or might not be changes in those characters which are not |
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| 398 | reconstructed. |
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| 399 | <P> |
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| 400 | For further information see the documentation files for the |
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| 401 | individual programs. |
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| 402 | </BODY> |
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| 403 | </HTML> |
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