                                  fconsense



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

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

Majority-rule and strict consensus tree
Version: EMBOSS:6.6.0.0

   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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit


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 3.69.650

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
                                          |
                                  +--6.00-|               +-------H
                                  |       |       +--4.00-|
                                  |       +--6.00-|       +-------J
                          +--2.00-|               |
                          |       |               +---------------D
                          |       |
                  +--6.00-|       |                       +-------F
                  |       |       +------------------9.00-|
                  |       |                               +-------I
          +--9.00-|       |
          |       |       +---------------------------------------G
  +-------|       |
  |       |       +-----------------------------------------------E
  |       |
  |       +-------------------------------------------------------B
  |
  +---------------------------------------------------------------A


  remember: this is an unrooted tree!


  File: consense.treefile

((((((C:9.00,((H:9.00,J:9.00):4.00,D:9.00):6.00):6.00,(F:9.00,I:9.00):9.00):2.00
,G:9.00):6.00,
E:9.00):9.00,B:9.00):9.00,A:9.00);

  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     Calculate distances between trees
   ftreedistpair    Calculate distance 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.

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) 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.

Comments

None
