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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>CONSENSE -- Consensus tree program</H1> |
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| 18 | </DIV> |
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| 19 | <P> |
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| 20 | © Copyright 1986-2000 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 | CONSENSE reads a file of computer-readable trees and prints |
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| 26 | out (and may also write out onto a file) a consensus tree. At the moment |
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| 27 | it carries out a family of consensus tree methods called the |
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| 28 | <I>M<SUB>l</SUB></I> |
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| 29 | methods (Margush and McMorris, 1981). These include strict consensus and |
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| 30 | majority rule consensus. Basically the |
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| 31 | consensus tree consists of monophyletic groups |
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| 32 | that occur as often as possible in the data. If a group occurs in more than |
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| 33 | a fraction <EM>l</EM> of all the input trees it will definitely |
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| 34 | appear in the consensus tree. |
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| 35 | <P> |
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| 36 | The tree printed out has at each fork a number indicating how many times the |
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| 37 | group which consists of the species to the right of (descended from) the fork |
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| 38 | occurred. Thus if we read in 15 trees and find that a fork has the number |
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| 39 | 15, that group occurred in all of the trees. The strict consensus tree |
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| 40 | consists of all groups that occurred 100% of the time, the rest of the |
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| 41 | resolution being ignored. The tree printed out here includes groups down |
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| 42 | to 50%, and below it until the tree is fully resolved. |
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| 43 | <P> |
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| 44 | The majority rule consensus tree consists of all groups that occur more than |
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| 45 | 50% of the time. Any other percentage level between 50% and 100% can also |
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| 46 | be used, and that is why the program in effect |
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| 47 | carries out a family of methods. You |
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| 48 | have to decide on the percentage level, figure out for yourself what number |
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| 49 | of occurrences that would be (e.g. 15 in the above case for 100%), and |
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| 50 | resolutely ignore any group below that number. Do not use numbers at or below |
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| 51 | 50%, because some groups occurring (say) 35% of the time will not be shown |
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| 52 | on the tree. The collection of all groups that occur 35% or more of the |
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| 53 | time may include two groups that are mutually self contradictory and cannot |
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| 54 | appear in the same tree. In this program, as the default method I have |
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| 55 | included groups that occur |
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| 56 | less than 50% of the time, working downwards in their frequency of occurrence, |
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| 57 | as long as they continue to resolve the tree and do not contradict more |
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| 58 | frequent groups. In this respect the method is similar to the Nelson consensus |
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| 59 | method (Nelson, 1979) as explicated by Page (1989) although it is not identical |
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| 60 | to it. |
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| 61 | <P> |
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| 62 | The program can also carry out Strict consensus, Majority Rule consensus |
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| 63 | without the extension which adds groups until the tree is fully |
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| 64 | resolved, and other members of the M<SUB>l</SUB> family, where the |
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| 65 | user supplied the fraction of times the group must appear in the input |
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| 66 | trees to be included in the consensus tree. |
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| 67 | For the moment the program cannot carry out any other |
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| 68 | consensus tree method, such as Adams consensus (Adams, 1972, 1986) or methods |
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| 69 | based on |
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| 70 | quadruples of species (Estabrook, McMorris, and Meacham, 1985). |
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| 71 | <P> |
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| 72 | <H2>INPUT, OUTPUT, AND OPTIONS</H2> |
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| 73 | <P> |
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| 74 | Input is a tree file (called <TT>intree</TT>) |
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| 75 | which contains a series of trees in the Newick |
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| 76 | standard form -- the form used when many of the programs in this package |
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| 77 | write out tree files. Each tree starts on a new line. Each tree can have |
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| 78 | a weight, which is a real number and is located in comment brackets "[" |
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| 79 | and "]" just before the final ";" which |
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| 80 | ends the description of the tree. When the input trees have weights |
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| 81 | (like [0.01000]) then the total number of trees will be the total of those |
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| 82 | weights, which is often a number like 1.00. When the a tree doesn't have |
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| 83 | a weight it will each be assigned a weight of 1. This means that when we have |
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| 84 | tied trees (as from a parsimony program) three alternative tied trees will |
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| 85 | be counted as if each was <SUP>1</SUP>/<SUB>3</SUB> of a tree. |
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| 86 | <P> |
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| 87 | Note that this program can correctly |
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| 88 | read trees whether or not they are bifurcating: in fact they can be |
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| 89 | multifurcating at any level in the tree. |
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| 90 | <P> |
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| 91 | The options are selected from a menu, which looks like this: |
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| 92 | <P> |
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| 93 | <TABLE><TR><TD BGCOLOR=white> |
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| 94 | <PRE> |
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| 95 | |
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| 96 | Majority-rule and strict consensus tree program, version 3.6 |
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| 97 | |
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| 98 | Settings for this run: |
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| 99 | C Consensus type (strict, MR, MRe, Ml) Majority Rule (extended) |
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| 100 | O Outgroup root: No, use as outgroup species 1 |
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| 101 | R Trees to be treated as Rooted: No |
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| 102 | T Terminal type (IBM PC, ANSI, none): none |
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| 103 | 1 Print out the sets of species: Yes |
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| 104 | 2 Print indications of progress of run: Yes |
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| 105 | 3 Print out tree: Yes |
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| 106 | 4 Write out trees onto tree file: Yes |
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| 107 | |
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| 108 | Are these settings correct? (type Y or the letter for one to change) |
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| 109 | </PRE> |
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| 110 | </TD></TR></TABLE> |
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| 111 | <P> |
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| 112 | Option C (Consensus method) selects which of four methods the |
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| 113 | program uses. The program defaults to using the extended Majority |
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| 114 | Rule method. Each time the C option is chosen the program moves on |
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| 115 | to another method, the others being in order Strict, Majority Rule, |
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| 116 | and M<SUB>l</SUB>. Here are descriptions of the methods. In each |
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| 117 | case the fraction of times a set appears among the input trees |
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| 118 | is counted by weighting by the weights of the trees (the numbers |
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| 119 | like <TT>[0.6000]</TT> that appear at the ends of trees in some |
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| 120 | cases). |
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| 121 | <P> |
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| 122 | <DL> |
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| 123 | <DT>Strict</DT> <DD>A set of species must appear in all input trees |
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| 124 | to be included in the strict consensus tree.</DD> |
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| 125 | <P> |
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| 126 | <DT>Majority Rule (extended)</DT> <DD>Any set of species that appears |
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| 127 | in more than 50% of the trees is included. The program then |
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| 128 | considers the other sets of species in order of the frequency with |
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| 129 | which they have appeared, adding to the consensus tree any which are |
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| 130 | compatible with it until the tree is fully resolved. This is the |
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| 131 | default setting.</DD> |
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| 132 | <P> |
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| 133 | <DT>M<SUB>l</SUB></DT> <DD>The user is asked for a fraction between |
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| 134 | 0.5 and 1, and the program then includes in the consensus tree any |
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| 135 | set of species that occurs among the input trees more than that |
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| 136 | fraction of then time. The Strict consensus and the Majority Rule |
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| 137 | consensus are extreme cases of the M<SUB>l</SUB> consensus, being |
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| 138 | for fractions of 1 and 0.5 respectively.</DD> |
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| 139 | <P> |
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| 140 | <DT>Majority Rule</DT> <DD>A set of species is included in the |
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| 141 | consensus tree if it is present in more than half of the |
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| 142 | input trees.</DD> |
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| 143 | </DL> |
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| 144 | <P> |
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| 145 | Option R (Rooted) toggles between the default assumption that the input trees |
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| 146 | are unrooted trees and the selection that |
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| 147 | specifies that the tree is to be treated as a rooted tree and not |
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| 148 | re-rooted. Otherwise the tree will be treated as outgroup-rooted and will |
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| 149 | be re-rooted automatically at the first species encountered on the first |
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| 150 | tree (or at a species designated by the Outgroup option). |
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| 151 | <P> |
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| 152 | Option O is the usual Outgroup rooting option. It is in effect only if |
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| 153 | the Rooted option selection is not in effect. The trees will be re-rooted |
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| 154 | with a species of your choosing. You will be asked for the number of the |
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| 155 | species that is to be the outgroup. If we want to outgroup-root the tree on |
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| 156 | the line leading to a |
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| 157 | species which appears as the third species (counting left-to-right) in the |
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| 158 | first computer-readable tree in the input file, we would invoke select |
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| 159 | menu option O and specify species 3. |
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| 160 | <P> |
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| 161 | Output is a list of the species (in the order in which they appear in the |
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| 162 | first tree, which is the numerical order used in the program), a list |
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| 163 | of the subsets that appear in the consensus tree, a list of those that |
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| 164 | appeared in one or another of the individual |
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| 165 | trees but did not occur frequently enough to get into the consensus tree, |
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| 166 | followed by a diagram showing the consensus tree. The lists of subsets |
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| 167 | consists of a row of symbols, each either "." or "*". The species |
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| 168 | that are in the set are marked by "*". Every ten species there is |
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| 169 | a blank, to help you keep track of the alignment of columns. The |
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| 170 | order of symbols corresponds to the order of species in the species |
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| 171 | list. Thus a set that consisted of the second, seventh, and eighth out |
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| 172 | of 13 species would be represented by: |
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| 173 | <P> |
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| 174 | <PRE> |
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| 175 | .*....**.. ... |
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| 176 | </PRE> |
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| 177 | <P> |
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| 178 | Note that if the trees are unrooted the final tree will have one group, |
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| 179 | consisting of every species except the Outgroup (which by default is the |
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| 180 | first species encountered on the first tree), which always appears. It |
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| 181 | will not be listed in either of the lists of sets, but it will be shown in |
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| 182 | the final tree as occurring all of the time. This is hardly surprising: |
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| 183 | in telling the program that this species is the outgroup we have specified |
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| 184 | that the set consisting of all of the others is always a monophyletic set. So |
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| 185 | this is not to be taken as interesting information, despite its dramatic |
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| 186 | appearance. |
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| 187 | <P> |
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| 188 | Option 2 in the menu gives you the option of turning off the writing of |
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| 189 | these sets into the output file. This may be useful if you are primarily |
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| 190 | interested in getting the tree file. |
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| 191 | <P> |
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| 192 | Option 3 is the usual tree file option. If this is on (it is by default) |
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| 193 | then the final tree will be written onto an output tree file (whose default |
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| 194 | name is "outtree"). Note that the lengths on the tree on the output tree file |
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| 195 | are not branch lengths but the number of times that |
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| 196 | each group appeared in the input trees. This |
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| 197 | number is the sum of the weights of the trees in which it appeared, so that |
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| 198 | if there are 11 trees, ten of them having weight 0.1 and one weight 1.0, |
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| 199 | a group that appeared in the last tree and in 6 others would be shown as |
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| 200 | appearing 1.6 times and its branch length will be 1.6. |
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| 201 | <P> |
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| 202 | <H2>CONSTANTS</H2> |
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| 203 | <P> |
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| 204 | The program uses the consensus tree algorithm originally designed for |
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| 205 | the bootstrap programs. It is quite fast, and execution time is unlikely |
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| 206 | to be limiting for you (assembling the input file will be much more of a |
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| 207 | limiting step). In the future, if possible, more consensus tree methods |
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| 208 | will be incorporated (although the current methods are the ones needed |
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| 209 | for the component analysis of bootstrap estimates of phylogenies, and in |
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| 210 | other respects I also think that the |
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| 211 | present ones are among the best). |
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| 212 | <P> |
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| 213 | <PRE> |
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| 214 | <P> |
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| 215 | <HR> |
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| 216 | <P> |
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| 217 | <H3>TEST DATA SET</H3> |
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| 218 | <P> |
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| 219 | <TABLE><TR><TD BGCOLOR=white> |
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| 220 | <PRE> |
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| 221 | (A,(B,(H,(D,(J,(((G,E),(F,I)),C)))))); |
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| 222 | (A,(B,(D,((J,H),(((G,E),(F,I)),C))))); |
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| 223 | (A,(B,(D,(H,(J,(((G,E),(F,I)),C)))))); |
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| 224 | (A,(B,(E,(G,((F,I),((J,(H,D)),C)))))); |
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| 225 | (A,(B,(E,(G,((F,I),(((J,H),D),C)))))); |
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| 226 | (A,(B,(E,((F,I),(G,((J,(H,D)),C)))))); |
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| 227 | (A,(B,(E,((F,I),(G,(((J,H),D),C)))))); |
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| 228 | (A,(B,(E,((G,(F,I)),((J,(H,D)),C))))); |
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| 229 | (A,(B,(E,((G,(F,I)),(((J,H),D),C))))); |
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| 230 | </PRE> |
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| 231 | </TD></TR></TABLE> |
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| 232 | <P> |
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| 233 | <HR> |
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| 234 | <P> |
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| 235 | <H3>TEST SET OUTPUT</H3> |
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| 236 | <P> |
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| 237 | <TABLE><TR><TD BGCOLOR=white> |
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| 238 | <PRE> |
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| 239 | |
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| 240 | Majority-rule and strict consensus tree program, version 3.6 |
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| 241 | |
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| 242 | Species in order: |
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| 243 | |
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| 244 | A |
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| 245 | B |
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| 246 | H |
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| 247 | D |
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| 248 | J |
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| 249 | G |
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| 250 | E |
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| 251 | F |
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| 252 | I |
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| 253 | C |
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| 254 | |
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| 255 | |
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| 256 | Sets included in the consensus tree |
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| 257 | |
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| 258 | Set (species in order) How many times out of 9.00 |
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| 259 | |
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| 260 | .......**. 9.00 |
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| 261 | ..******** 9.00 |
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| 262 | ..***....* 6.00 |
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| 263 | ..****.*** 6.00 |
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| 264 | ..***..... 6.00 |
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| 265 | ..*.*..... 4.00 |
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| 266 | ..***..*** 2.00 |
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| 267 | |
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| 268 | |
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| 269 | Sets NOT included in consensus tree: |
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| 270 | |
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| 271 | Set (species in order) How many times out of 9.00 |
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| 272 | |
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| 273 | .....**... 3.00 |
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| 274 | .....****. 3.00 |
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| 275 | ..**...... 3.00 |
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| 276 | .....***** 3.00 |
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| 277 | ..*.****** 2.00 |
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| 278 | .....*.**. 2.00 |
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| 279 | ..****...* 2.00 |
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| 280 | ....****** 2.00 |
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| 281 | ...******* 1.00 |
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| 282 | |
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| 283 | |
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| 284 | Majority rule consensus (extended to resolve tree) |
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| 285 | |
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| 286 | CONSENSUS TREE: |
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| 287 | the numbers at the forks indicate the number |
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| 288 | of times the group consisting of the species |
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| 289 | which are to the right of that fork occurred |
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| 290 | among the trees, out of 9.00 trees |
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| 291 | |
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| 292 | +-------------------------------------------------------A |
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| 293 | | |
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| 294 | | +-----------------------------------------E |
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| 295 | | | |
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| 296 | | | +------I |
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| 297 | | | +----------------9.0-| |
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| 298 | | | | +------F |
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| 299 | | +--9.0-| | |
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| 300 | | | | +--2.0-| +-------------D |
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| 301 | | | | | | +--6.0-| |
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| 302 | | | | | | | | +------J |
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| 303 | | | | | +--6.0-| +--4.0-| |
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| 304 | +------| +--6.0-| | +------H |
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| 305 | | | | |
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| 306 | | | +--------------------C |
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| 307 | | | |
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| 308 | | +----------------------------------G |
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| 309 | | |
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| 310 | +------------------------------------------------B |
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| 311 | |
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| 312 | |
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| 313 | remember: this is an unrooted tree! |
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| 314 | |
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| 315 | </PRE> |
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| 316 | </TD></TR></TABLE> |
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| 317 | </BODY> |
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| 318 | </HTML> |
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