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ffitch |
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Function
Fitch-Margoliash and Least-Squares Distance MethodsDescription
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
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| 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 | ||||||
| -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
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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
NoneNotes
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 |
|---|---|
| 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.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.