
                                 fconsense 



Function

   Majority-rule and strict consensus tree

Description

   Computes consensus trees by the majority-rule consensus tree method,
   which also allows one to easily find the strict consensus tree. Is not
   able to compute the Adams consensus tree. Trees are input in a tree
   file in standard nested-parenthesis notation, which is produced by
   many of the tree estimation programs in the package. This program can
   be used as the final step in doing bootstrap analyses for many of the
   methods in the package.

Algorithm

   fconsense reads a file of computer-readable trees and prints out (and
   may also write out onto a file) a consensus tree. At the moment it
   carries out a family of consensus tree methods called the Ml methods
   (Margush and McMorris, 1981). These include strict consensus and
   majority rule consensus. Basically the consensus tree consists of
   monophyletic groups that occur as often as possible in the data. If a
   group occurs in more than a fraction l of all the input trees it will
   definitely appear in the consensus tree.

   The tree printed out has at each fork a number indicating how many
   times the group which consists of the species to the right of
   (descended from) the fork occurred. Thus if we read in 15 trees and
   find that a fork has the number 15, that group occurred in all of the
   trees. The strict consensus tree consists of all groups that occurred
   100% of the time, the rest of the resolution being ignored. The tree
   printed out here includes groups down to 50%, and below it until the
   tree is fully resolved.

   The majority rule consensus tree consists of all groups that occur
   more than 50% of the time. Any other percentage level between 50% and
   100% can also be used, and that is why the program in effect carries
   out a family of methods. You have to decide on the percentage level,
   figure out for yourself what number of occurrences that would be (e.g.
   15 in the above case for 100%), and resolutely ignore any group below
   that number. Do not use numbers at or below 50%, because some groups
   occurring (say) 35% of the time will not be shown on the tree. The
   collection of all groups that occur 35% or more of the time may
   include two groups that are mutually self contradictory and cannot
   appear in the same tree. In this program, as the default method I have
   included groups that occur less than 50% of the time, working
   downwards in their frequency of occurrence, as long as they continue
   to resolve the tree and do not contradict more frequent groups. In
   this respect the method is similar to the Nelson consensus method
   (Nelson, 1979) as explicated by Page (1989) although it is not
   identical to it.

   The program can also carry out Strict consensus, Majority Rule
   consensus without the extension which adds groups until the tree is
   fully resolved, and other members of the Ml family, where the user
   supplied the fraction of times the group must appear in the input
   trees to be included in the consensus tree. For the moment the program
   cannot carry out any other consensus tree method, such as Adams
   consensus (Adams, 1972, 1986) or methods based on quadruples of
   species (Estabrook, McMorris, and Meacham, 1985).

Usage

   Here is a sample session with fconsense


% fconsense 
Majority-rule and strict consensus tree
Phylip tree file: consense.dat
Phylip consense program output file [consense.fconsense]: 


Consensus tree written to file "consense.treefile"

Output written to file "consense.fconsense"

Done.


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-intreefile]        tree       Phylip tree file
  [-outfile]           outfile    [*.fconsense] Phylip consense program output
                                  file

   Additional (Optional) qualifiers (* if not always prompted):
   -method             menu       [mre] Consensus method (Values: s (strict
                                  consensus tree); mr (Majority Rule); mre
                                  (Majority Rule (extended)); ml (Minimum
                                  fraction (0.5 to 1.0)))
*  -mlfrac             float      [0.5] Fraction (l) of times a branch must
                                  appear (Number from 0.500 to 1.000)
   -root               toggle     [N] Trees to be treated as Rooted
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.fconsense] Phylip tree output file
                                  (optional)
   -[no]progress       boolean    [Y] Print indications of progress of run
   -[no]treeprint      boolean    [Y] Print out tree
   -[no]prntsets       boolean    [Y] Print out the sets of species

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-outtreefile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   fconsense reads any normal sequence USAs.

  Input files for usage example

  File: consense.dat

(A,(B,(H,(D,(J,(((G,E),(F,I)),C))))));
(A,(B,(D,((J,H),(((G,E),(F,I)),C)))));
(A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));
(A,(B,(E,(G,((F,I),((J,(H,D)),C))))));
(A,(B,(E,(G,((F,I),(((J,H),D),C))))));
(A,(B,(E,((F,I),(G,((J,(H,D)),C))))));
(A,(B,(E,((F,I),(G,(((J,H),D),C))))));
(A,(B,(E,((G,(F,I)),((J,(H,D)),C)))));
(A,(B,(E,((G,(F,I)),(((J,H),D),C)))));

Output file format

   fconsense output is a list of the species (in the order in which they
   appear in the first tree, which is the numerical order used in the
   program), a list of the subsets that appear in the consensus tree, a
   list of those that appeared in one or another of the individual trees
   but did not occur frequently enough to get into the consensus tree,
   followed by a diagram showing the consensus tree. The lists of subsets
   consists of a row of symbols, each either "." or "*". The species that
   are in the set are marked by "*". Every ten species there is a blank,
   to help you keep track of the alignment of columns. The order of
   symbols corresponds to the order of species in the species list. Thus
   a set that consisted of the second, seventh, and eighth out of 13
   species would be represented by:

          .*....**.. ...

   Note that if the trees are unrooted the final tree will have one
   group, consisting of every species except the Outgroup (which by
   default is the first species encountered on the first tree), which
   always appears. It will not be listed in either of the lists of sets,
   but it will be shown in the final tree as occurring all of the time.
   This is hardly surprising: in telling the program that this species is
   the outgroup we have specified that the set consisting of all of the
   others is always a monophyletic set. So this is not to be taken as
   interesting information, despite its dramatic appearance.

  Output files for usage example

  File: consense.fconsense


Consensus tree program, version 3.6b

Species in order:

  1. A
  2. B
  3. H
  4. D
  5. J
  6. G
  7. E
  8. F
  9. I
  10. C



Sets included in the consensus tree

Set (species in order)     How many times out of    9.00

.......**.                   9.00
..********                   9.00
..****.***                   6.00
..***.....                   6.00
..***....*                   6.00
..*.*.....                   4.00
..***..***                   2.00


Sets NOT included in consensus tree:

Set (species in order)     How many times out of    9.00

.....**...                   3.00
.....*****                   3.00
..**......                   3.00
.....****.                   3.00
..****...*                   2.00
.....*.**.                   2.00
..*.******                   2.00
....******                   2.00
...*******                   1.00


Extended majority rule consensus tree

CONSENSUS TREE:
the numbers on the branches indicate the number
of times the partition of the species into the two sets
which are separated by that branch occurred
among the trees, out of   9.00 trees

                                     +--------------------C
                                     |
                              +--6.0-|             +------H
                              |      |      +--4.0-|
                              |      +--6.0-|      +------J
                       +--2.0-|             |
                       |      |             +-------------D
                       |      |
                +--6.0-|      |                    +------F
                |      |      +----------------9.0-|
                |      |                           +------I
         +--9.0-|      |
         |      |      +----------------------------------G
  +------|      |
  |      |      +-----------------------------------------E
  |      |
  |      +------------------------------------------------B
  |
  +-------------------------------------------------------A


  remember: this is an unrooted tree!

  File: consense.treefile

((((((C:9.0,((H:9.0,J:9.0):4.0,D:9.0):6.0):6.0,(F:9.0,I:9.0):9.0):2.0,G:9.0):6.
0,E:9.0):9.0,
B:9.0):9.0,A:9.0);

  Branch Lengths on the Consensus Tree?

   Note that the lengths on the tree on the output tree file are not
   branch lengths but the number of times that each group appeared in the
   input trees. This number is the sum of the weights of the trees in
   which it appeared, so that if there are 11 trees, ten of them having
   weight 0.1 and one weight 1.0, a group that appeared in the last tree
   and in 6 others would be shown as appearing 1.6 times and its branch
   length will be 1.6. This means that if you take the consensus tree
   from the output tree file and try to draw it, the branch lengths will
   be strange. I am often asked how to put the correct branch lengths on
   these (this is one of our Frequently Asked Questions). There is no
   simple answer to this. It depends on what "correct" means. For
   example, if you have a group of species that shows up in 80% of the
   trees, and the branch leading to that group has average length 0.1
   among that 80%, is the "correct" length 0.1? Or is it (0.80 x 0.1)?
   There is no simple answer. However, if you want to take the consensus
   tree as an estimate of the true tree (rather than as an indicator of
   the conflicts among trees) you may be able to use the User Tree
   (option U) mode of the phylogeny program that you used, and use it to
   put branch lengths on that tree. Thus, if you used DNAML, you can take
   the consensus tree, make sure it is an unrooted tree, and feed that to
   DNAML using the original data set (before bootstrapping) and DNAML's
   option U. As DNAML wants an unrooted tree, you may have to use RETREE
   to make the tree unrooted (using the W option of RETREE and choosing
   the unrooted option within it). Of course you will also want to change
   the tree file name from "outree" to "intree". If you used a phylogeny
   program that does not infer branch lengths, you might want to use a
   different one (such as FITCH or DNAML) to infer the branch lengths,
   again making sure the tree is unrooted, if the program needs that.

Data files

   None

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                Description
   econsense     Majority-rule and strict consensus tree
   ftreedist     Distances between trees
   ftreedistpair Distances between two sets of trees

Author(s)

   This program is an EMBOSS conversion of a program written by Joe
   Felsenstein as part of his PHYLIP package.

   Although we take every care to ensure that the results of the EMBOSS
   version are identical to those from the original package, we recommend
   that you check your inputs give the same results in both versions
   before publication.

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   not to the original author.

History

   Written (2004) - Joe Felsenstein, University of Washington.

   Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
