ffitch 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 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:6.6.0.0 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 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 3.69.650 __ __ 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. 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 (c) 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