EMBOSS: ffitch

ffitch

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Function

Fitch-Margoliash and Least-Squares Distance Methods

Description

Estimates phylogenies from distance matrix data under the "additive tree model" according to which the distances are expected to equal the sums of branch lengths between the species. Uses the Fitch-Margoliash criterion and some related least squares criteria, or the Minimum Evolution distance matrix method. Does not assume an evolutionary clock. This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with DNA hybridization measurements, and with genetic distances computed from gene frequencies.

Algorithm

The programs FITCH, KITSCH, and NEIGHBOR are for dealing with data which comes in the form of a matrix of pairwise distances between all pairs of taxa, such as distances based on molecular sequence data, gene frequency genetic distances, amounts of DNA hybridization, or immunological distances. In analyzing these data, distance matrix programs implicitly assume that:

Each distance is measured independently from the others: no item of data contributes to more than one distance.
The distance between each pair of taxa is drawn from a distribution with an expectation which is the sum of values (in effect amounts of evolution) along the tree from one tip to the other. The variance of the distribution is proportional to a power p of the expectation.

These assumptions can be traced in the least squares methods of programs FITCH and KITSCH but it is not quite so easy to see them in operation in the Neighbor-Joining method of NEIGHBOR, where the independence assumptions is less obvious.

THESE TWO ASSUMPTIONS ARE DUBIOUS IN MOST CASES: independence will not be expected to be true in most kinds of data, such as genetic distances from gene frequency data. For genetic distance data in which pure genetic drift without mutation can be assumed to be the mechanism of change CONTML may be more appropriate. However, FITCH, KITSCH, and NEIGHBOR will not give positively misleading results (they will not make a statistically inconsistent estimate) provided that additivity holds, which it will if the distance is computed from the original data by a method which corrects for reversals and parallelisms in evolution. If additivity is not expected to hold, problems are more severe. A short discussion of these matters will be found in a review article of mine (1984a). For detailed, if sometimes irrelevant, controversy see the papers by Farris (1981, 1985, 1986) and myself (1986, 1988b).

For genetic distances from gene frequencies, FITCH, KITSCH, and NEIGHBOR may be appropriate if a neutral mutation model can be assumed and Nei's genetic distance is used, or if pure drift can be assumed and either Cavalli-Sforza's chord measure or Reynolds, Weir, and Cockerham's (1983) genetic distance is used. However, in the latter case (pure drift) CONTML should be better.

Restriction site and restriction fragment data can be treated by distance matrix methods if a distance such as that of Nei and Li (1979) is used. Distances of this sort can be computed in PHYLIp by the program RESTDIST.

For nucleic acid sequences, the distances computed in DNADIST allow correction for multiple hits (in different ways) and should allow one to analyse the data under the presumption of additivity. In all of these cases independence will not be expected to hold. DNA hybridization and immunological distances may be additive and independent if transformed properly and if (and only if) the standards against which each value is measured are independent. (This is rarely exactly true).

FITCH and the Neighbor-Joining option of NEIGHBOR fit a tree which has the branch lengths unconstrained. KITSCH and the UPGMA option of NEIGHBOR, by contrast, assume that an "evolutionary clock" is valid, according to which the true branch lengths from the root of the tree to each tip are the same: the expected amount of evolution in any lineage is proportional to elapsed time.

Usage

Here is a sample session with ffitch

% ffitch Fitch-Margoliash and Least-Squares Distance Methods Phylip distance matrix file: fitch.dat Phylip tree file (optional): Phylip fitch program output file [fitch.ffitch]: Adding species: 1. Bovine 2. Mouse 3. Gibbon 4. Orang 5. Gorilla 6. Chimp 7. Human Output written to file "fitch.ffitch" Tree also written onto file "fitch.treefile" Done.

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

Command line arguments

Fitch-Margoliash and Least-Squares Distance Methods
Version: EMBOSS:6.3.0

   Standard (Mandatory) qualifiers:
  [-datafile]          distances  File containing one or more distance
                                  matrices
  [-intreefile]        tree       Phylip tree file (optional)
  [-outfile]           outfile    [*.ffitch] Phylip fitch program output file

   Additional (Optional) qualifiers (* if not always prompted):
   -matrixtype         menu       [s] Type of input data matrix (Values: s
                                  (Square); u (Upper triangular); l (Lower
                                  triangular))
   -minev              boolean    [N] Minimum evolution
*  -njumble            integer    [0] Number of times to randomise (Integer 0
                                  or more)
*  -seed               integer    [1] Random number seed between 1 and 32767
                                  (must be odd) (Integer from 1 to 32767)
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -power              float      [2.0] Power (Any numeric value)
*  -lengths            boolean    [N] Use branch lengths from user trees
*  -negallowed         boolean    [N] Negative branch lengths allowed
*  -global             boolean    [N] Global rearrangements
   -replicates         boolean    [N] Subreplicates
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.ffitch] Phylip tree output file
                                  (optional)
   -printdata          boolean    [N] Print data at start of run
   -[no]progress       boolean    [Y] Print indications of progress of run
   -[no]treeprint      boolean    [Y] Print out tree

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

   "-outfile" associated qualifiers
   -odirectory3        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

[-datafile]
(Parameter 1) distances File containing one or more distance matrices Distance matrix

[-intreefile]
(Parameter 2) tree Phylip tree file (optional) Phylogenetic tree

[-outfile]
(Parameter 3) outfile Phylip fitch program output file Output file <*>.ffitch

Additional (Optional) qualifiers

-matrixtype list Type of input data matrix
s (Square)
u (Upper triangular)
l (Lower triangular)
s

-minev boolean Minimum evolution Boolean value Yes/No No

-njumble integer Number of times to randomise Integer 0 or more 0

-seed integer Random number seed between 1 and 32767 (must be odd) Integer from 1 to 32767 1

-outgrno integer Species number to use as outgroup Integer 0 or more 0

-power float Power Any numeric value 2.0

-lengths boolean Use branch lengths from user trees Boolean value Yes/No No

-negallowed boolean Negative branch lengths allowed Boolean value Yes/No No

-global boolean Global rearrangements Boolean value Yes/No No

-replicates boolean Subreplicates Boolean value Yes/No No

-[no]trout toggle Write out trees to tree file Toggle value Yes/No Yes

-outtreefile outfile Phylip tree output file (optional) Output file <*>.ffitch

-printdata boolean Print data at start of run Boolean value Yes/No No

-[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

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-outfile" associated outfile qualifiers

-odirectory3
-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

ffitch reads any normal sequence USAs.

Input files for usage example

File: fitch.dat

    7
Bovine      0.0000  1.6866  1.7198  1.6606  1.5243  1.6043  1.5905
Mouse       1.6866  0.0000  1.5232  1.4841  1.4465  1.4389  1.4629
Gibbon      1.7198  1.5232  0.0000  0.7115  0.5958  0.6179  0.5583
Orang       1.6606  1.4841  0.7115  0.0000  0.4631  0.5061  0.4710
Gorilla     1.5243  1.4465  0.5958  0.4631  0.0000  0.3484  0.3083
Chimp       1.6043  1.4389  0.6179  0.5061  0.3484  0.0000  0.2692
Human       1.5905  1.4629  0.5583  0.4710  0.3083  0.2692  0.0000

Output file format

ffitch output consists of an unrooted tree and the lengths of the interior segments. The sum of squares is printed out, and if P = 2.0 Fitch and Margoliash's "average percent standard deviation" is also computed and printed out. This is the sum of squares, divided by N-2, and then square-rooted and then multiplied by 100 (n is the number of species on the tree):

     APSD = ( SSQ / (N-2) )1/2 x 100.

where N is the total number of off-diagonal distance measurements that are in the (square) distance matrix. If the S (subreplication) option is in force it is instead the sum of the numbers of replicates in all the non-diagonal cells of the distance matrix. But if the L or R option is also in effect, so that the distance matrix read in is lower- or upper-triangular, then the sum of replicates is only over those cells actually read in. If S is not in force, the number of replicates in each cell is assumed to be 1, so that N is n(n-1), where n is the number of species. The APSD gives an indication of the average percentage error. The number of trees examined is also printed out.

Output files for usage example

File: fitch.ffitch


   7 Populations

Fitch-Margoliash method version 3.69

                  __ __             2
                  \  \   (Obs - Exp)
Sum of squares =  /_ /_  ------------
                                2
                   i  j      Obs

Negative branch lengths not allowed


  +---------------------------------------------Mouse     
  ! 
  !                                +------Human     
  !                             +--5 
  !                           +-4  +--------Chimp     
  !                           ! ! 
  !                        +--3 +---------Gorilla   
  !                        !  ! 
  1------------------------2  +-----------------Orang     
  !                        ! 
  !                        +---------------------Gibbon    
  ! 
  +------------------------------------------------------Bovine    


remember: this is an unrooted tree!

Sum of squares =     0.01375

Average percent standard deviation =     1.85418

Between        And            Length
-------        ---            ------
   1          Mouse             0.76985
   1             2              0.41983
   2             3              0.04986
   3             4              0.02121
   4             5              0.03695
   5          Human             0.11449
   5          Chimp             0.15471
   4          Gorilla           0.15680
   3          Orang             0.29209
   2          Gibbon            0.35537
   1          Bovine            0.91675

File: fitch.treefile

(Mouse:0.76985,((((Human:0.11449,Chimp:0.15471):0.03695,
Gorilla:0.15680):0.02121,Orang:0.29209):0.04986,Gibbon:0.35537):0.41983,Bovine:0.91675);

Data files

None

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
efitch	Fitch-Margoliash and Least-Squares Distance Methods
ekitsch	Fitch-Margoliash method with contemporary tips
eneighbor	Phylogenies from distance matrix by N-J or UPGMA method
fkitsch	Fitch-Margoliash method with contemporary tips
fneighbor	Phylogenies from distance matrix by N-J or UPGMA method

Author(s)

This program is an EMBOSS conversion of a program written by Joe Felsenstein as part of his PHYLIP package.

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.

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: fitch.dat

Output file format

Output files for usage example

File: fitch.ffitch

File: fitch.treefile

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users