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EMBOSS: fconsense
fconsense

 

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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:6.3.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-intreefile]
(Parameter 1)		 tree Phylip tree file Phylogenetic tree  
[-outfile]
(Parameter 2)		 outfile Phylip consense program output file Output file <*>.fconsense
Additional (Optional) qualifiers
-method list Consensus method
s (strict consensus tree)
mr (Majority Rule)
mre (Majority Rule (extended))
ml (Minimum fraction (0.5 to 1.0))
 mre
-mlfrac float Fraction (l) of times a branch must appear Number from 0.500 to 1.000 0.5
-root toggle Trees to be treated as Rooted Toggle value Yes/No No
-outgrno integer Species number to use as outgroup Integer 0 or more 0
-[no]trout toggle Write out trees to tree file Toggle value Yes/No Yes
-outtreefile outfile Phylip tree output file (optional) Output file <*>.fconsense
-[no]progress boolean Print indications of progress of run Boolean value Yes/No Yes
-[no]treeprint boolean Print out tree Boolean value Yes/No Yes
-[no]prntsets boolean Print out the sets of species Boolean value Yes/No Yes
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
"-outtreefile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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

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 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.

Please report all bugs to the EMBOSS bug team (emboss-bug © 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.