fconsense |
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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. |
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Majority-rule and strict consensus tree Version: EMBOSS:6.4.0.0 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 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 | Distances between trees |
ftreedistpair | Distances 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.