EMBOSS: ftreedist

| ftreedist

## 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

Calculate distances between trees

## Description

Computes the Branch Score distance between trees, which allows for differences in tree topology and which also makes use of branch lengths. Also computes the Robinson-Foulds symmetric difference distance between trees, which allows for differences in tree topology but does not use branch lengths.

## Algorithm

This program computes distances between trees. Two distances are computed, the Branch Score Distance of Kuhner and Felsenstein (1994), and the more widely known Symmetric Difference of Robinson and Foulds (1981). The Branch Score Distance uses branch lengths, and can only be calculated when the trees have lengths on all branches. The Symmetric Difference does not use branch length information, only the tree topologies. It must also be borne in mind that neither distance has any immediate statistical interpretation -- we cannot say whether a larger distance is significantly larger than a smaller one.

These distances are computed by considering all possible branches that could exist on the the two trees. Each branch divides the set of species into two groups -- the ones connected to one end of the branch and the ones connected to the other. This makes a partition of the full set of species. (in Newick notation)

      ((A,C),(D,(B,E)))

has two internal branches. One induces the partition {A, C | B, D, E} and the other induces the partition {A, C, D | B, E}. A different tree with the same set of species,

      (((A,D),C),(B,E))

has internal branches that correspond to the two partitions {A, C, D | B, E} and {A, D | B, C, E}. Note that the other branches, all of which are external branches, induce partitions that separate one species from all the others. Thus there are 5 partitions like this: {C | A, B, D, E} on each of these trees. These are always present on all trees, provided that each tree has each species at the end of its own branch.

In the case of the Branch Score distance, each partition that does exist on a tree also has a branch length associated with it. Thus if the tree is

      (((A:0.1,D:0.25):0.05,C:0.01):0.2,(B:0.3,E:0.8):0.2)

The list of partitions and their branch lengths is:

    {A  |  B, C, D, E}     0.1
    {D  |  A, B, C, E}     0.25
    {A, D  |  B, C, E}     0.05
    {C  |  A, B, D, E}     0.01
    {A, D, C  |  B, E}     0.4
    {B  |  A, C, D, E}     0.3
    {E  |  A, B, C, D}     0.8

Note that the tree is being treated as unrooted here, so that the branch lengths on either side of the rootmost node are summed up to get a branch length of 0.4.

The Branch Score Distance imagines us as having made a list of all possible partitions, the ones shown above and also all 7 other possible partitions, which correspond to branches that are not found in this tree. These are assigned branch lengths of 0. For two trees, we imagine constructing these lists, and then summing the squared differences between the branch lengths. Thus if both trees have branches {A, D | B, C, E}, the sum contains the square of the difference between the branch lengths. If one tree has the branch and the other doesn't, it contains the square of the difference between the branch length and zero (in other words, the square of that branch length). If both trees do not have a particular branch, nothing is added to the sum because the difference is then between 0 and 0.

The Branch Score Distance takes this sum of squared differences and computes its square root. Note that it has some desirable properties. When small branches differ in tree topology, it is not very big. When branches are both present but differ in length, it is affected.

The Symmetric Difference is simply a count of how many partitions there are, among the two trees, that are on one tree and not on the other. In the example above there are two partitions, {A, C | B, D, E} and {A, D | B, C, E}, each of which is present on only one of the two trees. The Symmetric Difference between the two trees is therefore 2. When the two trees are fully resolved bifurcating trees, their symmetric distance must be an even number; it can range from 0 to twice the number of internal branches, which for n species is 4n-6.

Note the relationship between the two distances. If all trees have all their branches have length 1.0, the Branch Score Distance is the square of the Symmetric Difference, as each branch that is present in one but not in the other results in 1.0 being added to the sum of squared differences.

We have assumed that nothing is lost if the trees are treated as unrooted trees. It is easy to define a counterpart to the Branch Score Distance and one to the Symmetric Difference for these rooted trees. Each branch then defines a set of species, namely the clade defined by that branch. Thus if the first of the two trees above were considered as a rooted tree it would define the three clades {A, C}, {B, D, E}, and {B, E}. The Branch Score Distance is computed from the branch lengths for all possible sets of species, with 0 put for each set that does not occur on that tree. The table above will be nearly the same, but with two entries instead of one for the sets on either side of the root, {A C D} and {B E}. The Symmetric Difference between two rooted trees is simply the count of the number of clades that are defined by one but not by the other. For the second tree the clades would be {A, D}, {B, C, E}, and {B, E}. The Symmetric Difference between thee two rooted trees would then be 4.

Although the examples we have discussed have involved fully bifurcating trees, the input trees can have multifurcations. This does not cause any complication for the Branch Score Distance. For the Symmetric Difference, it can lead to distances that are odd numbers.

However, note one strong restriction. The trees should all have the same list of species. If you use one set of species in the first two trees, and another in the second two, and choose distances for adjacent pairs, the distances will be incorrect and will depend on the order of these pairs in the input tree file, in odd ways.

## Usage

Here is a sample session with ftreedist

    % ftreedist
    Calculate distances between trees
    Phylip tree file: treedist.dat
    Phylip treedist program output file [treedist.ftreedist]:

    Output written to file "treedist.ftreedist"

    Done.

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

Example 2

    % ftreedist -dtype s
    Calculate distances between trees
    Phylip tree file: treedist2.dat
    Phylip treedist program output file [treedist2.ftreedist]:

    Output written to file "treedist2.ftreedist"

    Done.

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

## Command line arguments

    Calculate distances between trees
    Version: EMBOSS:6.6.0.0

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

       Additional (Optional) qualifiers:
       -dtype              menu       [b] Distance type (Values: s (Symmetric
                                      difference); b (Branch score distance))
       -pairing            menu       [a] Tree pairing method (Values: a
                                      (Distances between adjacent pairs in tree
                                      file); p (Distances between all possible
                                      pairs in tree file))
       -style              menu       [v] Distances output option (Values: f (Full
                                      matrix); v (Verbose, one pair per line); s
                                      (Sparse, one pair per line))
       -noroot             boolean    [N] Trees to be treated as rooted
       -outgrno            integer    [0] Species number to use as outgroup
                                      (Integer 0 or more)
       -[no]progress       boolean    [Y] Print indications of progress of run

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

       "-outfile" associated qualifiers
       -odirectory2        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 treedist program output file | Output file | <*>.ftreedist
Additional (Optional) qualifiers
-dtype | list | Distance type |
s | (Symmetric difference)
b | (Branch score distance)
| b
-pairing | list | Tree pairing method |
a | (Distances between adjacent pairs in tree file)
p | (Distances between all possible pairs in tree file)
| a
-style | list | Distances output option |
f | (Full matrix)
v | (Verbose, one pair per line)
s | (Sparse, one pair per line)
| v
-noroot | boolean | Trees to be treated as rooted | Boolean value Yes/No | No
-outgrno | integer | Species number to use as outgroup | Integer 0 or more | 0
-[no]progress | boolean | Print indications of progress of run | Boolean value Yes/No | Yes
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile | 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

ftreedist reads one input tree file. If the number of trees is given, it is actually ignored and all trees in the tree file are considered, even if there are more trees than indicated by the number. There is no maximum number of trees that can be processed but, if you feed in too many, there may be an error message about running out of memory. The problem is particularly acute if you choose the option to examine all possible pairs of trees in an input tree file. Thus if there are 1,000 trees in the input tree file, keep in mind that all possible pairs means 1,000,000 pairs to be examined!

### Input files for usage example

### File: treedist.dat

    (A:0.1,(B:0.1,(H:0.1,(D:0.1,(J:0.1,(((G:0.1,E:0.1):0.1,(F:0.1,I:0.1):0.1):0.1,
    C:0.1):0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(D:0.1,((J:0.1,H:0.1):0.1,(((G:0.1,E:0.1):0.1,
    (F:0.1,I:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(D:0.1,(H:0.1,(J:0.1,(((G:0.1,E:0.1):0.1,(F:0.1,I:0.1):0.1):0.1,
    C:0.1):0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(E:0.1,(G:0.1,((F:0.1,I:0.1):0.1,((J:0.1,(H:0.1,D:0.1):0.1):0.1,
    C:0.1):0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(E:0.1,(G:0.1,((F:0.1,I:0.1):0.1,(((J:0.1,H:0.1):0.1,D:0.1):0.1,
    C:0.1):0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(E:0.1,((F:0.1,I:0.1):0.1,(G:0.1,((J:0.1,(H:0.1,D:0.1):0.1):0.1,
    C:0.1):0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(E:0.1,((F:0.1,I:0.1):0.1,(G:0.1,(((J:0.1,H:0.1):0.1,D:0.1):0.1,
    C:0.1):0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(E:0.1,((G:0.1,(F:0.1,I:0.1):0.1):0.1,((J:0.1,(H:0.1,
    D:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(E:0.1,((G:0.1,(F:0.1,I:0.1):0.1):0.1,(((J:0.1,H:0.1):0.1,
    D:0.1):0.1,C:0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(E:0.1,(G:0.1,((F:0.1,I:0.1):0.1,((J:0.1,(H:0.1,D:0.1):0.1):0.1,
    C:0.1):0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(D:0.1,(H:0.1,(J:0.1,(((G:0.1,E:0.1):0.1,(F:0.1,I:0.1):0.1):0.1,
    C:0.1):0.1):0.1):0.1):0.1):0.1);
    (A:0.1,(B:0.1,(E:0.1,((G:0.1,(F:0.1,I:0.1):0.1):0.1,((J:0.1,(H:0.1,
    D:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1);

### Input files for usage example 2

### File: treedist2.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)))));
    (A,(B,(E,(G,((F,I),((J,(H,D)),C))))));
    (A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));
    (A,(B,(E,((G,(F,I)),((J,(H,D)),C)))));

## Output file format

If any of the four types of analysis are selected, the user must specify how they want the results presented.

The Full matrix (choice F) is a table showing all distances. It is written onto the output file. The table is presented as groups of 10 columns. Here is the Full matrix for the 12 trees in the input tree file which is given as an example at the end of this page.

    Tree distance program, version 3.6

    Symmetric differences between all pairs of trees in tree file:

              1     2     3     4     5     6     7     8     9    10
          \------------------------------------------------------------
        1 |   0     4     2    10    10    10    10    10    10    10
        2 |   4     0     2    10     8    10     8    10     8    10
        3 |   2     2     0    10    10    10    10    10    10    10
        4 |  10    10    10     0     2     2     4     2     4     0
        5 |  10     8    10     2     0     4     2     4     2     2
        6 |  10    10    10     2     4     0     2     2     4     2
        7 |  10     8    10     4     2     2     0     4     2     4
        8 |  10    10    10     2     4     2     4     0     2     2
        9 |  10     8    10     4     2     4     2     2     0     4
       10 |  10    10    10     0     2     2     4     2     4     0
       11 |   2     2     0    10    10    10    10    10    10    10
       12 |  10    10    10     2     4     2     4     0     2     2

             11    12
          \------------
        1 |   2    10
        2 |   2    10
        3 |   0    10
        4 |  10     2
        5 |  10     4
        6 |  10     2
        7 |  10     4
        8 |  10     0
        9 |  10     2
       10 |  10     2
       11 |   0    10
       12 |  10     0

The Full matrix is only available for analyses P and L (not for A or C).

Option V (Verbose) writes one distance per line. The Verbose output is the default. Here it is for the example data set given below:

    Tree distance program, version 3.6

    Symmetric differences between adjacent pairs of trees:

    Trees 1 and 2:    4
    Trees 3 and 4:    10
    Trees 5 and 6:    4
    Trees 7 and 8:    4
    Trees 9 and 10:    4
    Trees 11 and 12:    10

Option S (Sparse or terse) is similar except that all that is given on each line are the numbers of the two trees and the distance, separated by blanks. This may be a convenient format if you want to write a program to read these numbers in, and you want to spare yourself the effort of having the program wade through the words on each line in the Verbose output. The first four lines of the Sparse output are titles that your program would want to skip past. Here is the Sparse output for the example trees.

    1 2 4
    3 4 10
    5 6 4
    7 8 4
    9 10 4
    11 12 10

### Output files for usage example

### File: treedist.ftreedist

    Tree distance program, version 3.69.650

    Branch score distances between adjacent pairs of trees:

    Trees 1 and 2:    2.000000e-01
    Trees 3 and 4:    3.162278e-01
    Trees 5 and 6:    2.000000e-01
    Trees 7 and 8:    2.000000e-01
    Trees 9 and 10:    2.000000e-01
    Trees 11 and 12:    3.162278e-01

### Output files for usage example 2

### File: treedist2.ftreedist

    Tree distance program, version 3.69.650

    Symmetric differences between adjacent pairs of trees:

    Trees 1 and 2:    4
    Trees 3 and 4:    10
    Trees 5 and 6:    4
    Trees 7 and 8:    4
    Trees 9 and 10:    4
    Trees 11 and 12:    10

## 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
fconsense | Majority-rule and strict consensus tree
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 © 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