|   | fconsense | 
Please help by correcting and extending the Wiki pages.
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).
| % 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
| 
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
 | 
| 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 | 
 | 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 | ||||||||
| (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))))); | 
          .*....**.. ...
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.
| 
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!
 | 
| ((((((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); | 
| Program name | Description | 
|---|---|
| econsense | Majority-rule and strict consensus tree | 
| ftreedist | Calculate distances between trees | 
| ftreedistpair | Calculate distance between two sets of trees | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.
None