fdnacomp 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 DNA compatibility algorithm Description Estimates phylogenies from nucleic acid sequence data using the compatibility criterion, which searches for the largest number of sites which could have all states (nucleotides) uniquely evolved on the same tree. Compatibility is particularly appropriate when sites vary greatly in their rates of evolution, but we do not know in advance which are the less reliable ones. Algorithm This program implements the compatibility method for DNA sequence data. For a four-state character without a character-state tree, as in DNA sequences, the usual clique theorems cannot be applied. The approach taken in this program is to directly evaluate each tree topology by counting how many substitutions are needed in each site, comparing this to the minimum number that might be needed (one less than the number of bases observed at that site), and then evaluating the number of sites which achieve the minimum number. This is the evaluation of the tree (the number of compatible sites), and the topology is chosen so as to maximize that number. Compatibility methods originated with Le Quesne's (1969) suggestion that one ought to look for trees supported by the largest number of perfectly fitting (compatible) characters. Fitch (1975) showed by counterexample that one could not use the pairwise compatibility methods used in CLIQUE to discover the largest clique of jointly compatible characters. The assumptions of this method are similar to those of CLIQUE. In a paper in the Biological Journal of the Linnean Society (1981b) I discuss this matter extensively. In effect, the assumptions are that: 1. Each character evolves independently. 2. Different lineages evolve independently. 3. The ancestral base at each site is unknown. 4. The rates of change in most sites over the time spans involved in the the divergence of the group are very small. 5. A few of the sites have very high rates of change. 6. We do not know in advance which are the high and which the low rate sites. That these are the assumptions of compatibility methods has been documented in a series of papers of mine: (1973a, 1978b, 1979, 1981b, 1983b, 1988b). For an opposing view arguing that arguments such as mine are invalid and that parsimony (and perhaps compatibility) methods make no substantive assumptions such as these, see the papers by Farris (1983) and Sober (1983a, 1983b, 1988), but also read the exchange between Felsenstein and Sober (1986). There is, however, some reason to believe that the present criterion is not the proper way to correct for the presence of some sites with high rates of change in nucleotide sequence data. It can be argued that sites showing more than two nucleotide states, even if those are compatible with the other sites, are also candidates for sites with high rates of change. It might then be more proper to use DNAPARS with the Threshold option with a threshold value of 2. Change from an occupied site to a gap is counted as one change. Reversion from a gap to an occupied site is allowed and is also counted as one change. Note that this in effect assumes that a gap N bases long is N separate events. This may be an overcorrection. When we have nonoverlapping gaps, we could instead code a gap as a single event by changing all but the first "-" in the gap into "?" characters. In this way only the first base of the gap causes the program to infer a change. If the U (User Tree) option is used and more than one tree is supplied, the program also performs a statistical test of each of these trees against the one with highest likelihood. If there are two user trees, the test done is one which is due to Kishino and Hasegawa (1989), a version of a test originally introduced by Templeton (1983). In this implementation it uses the mean and variance of weighted compatibility differences between trees, taken across sites. If the two trees compatibilities are more than 1.96 standard deviations different then the trees are declared significantly different. If there are more than two trees, the test done is an extension of the KHT test, due to Shimodaira and Hasegawa (1999). They pointed out that a correction for the number of trees was necessary, and they introduced a resampling method to make this correction. In the version used here the variances and covariances of the sum of weighted compatibilities of sites are computed for all pairs of trees. To test whether the difference between each tree and the best one is larger than could have been expected if they all had the same expected compatibility, compatibilities for all trees are sampled with these covariances and equal means (Shimodaira and Hasegawa's "least favorable hypothesis"), and a P value is computed from the fraction of times the difference between the tree's value and the highest compatibility exceeds that actually observed. Note that this sampling needs random numbers, and so the program will prompt the user for a random number seed if one has not already been supplied. With the two-tree KHT test no random numbers are used. In either the KHT or the SH test the program prints out a table of the compatibility of each tree, the differences of each from the highest one, the variance of that quantity as determined by the compatibility differences at individual sites, and a conclusion as to whether that tree is or is not significantly worse than the best one. The algorithm is a straightforward modification of DNAPARS, but with some extra machinery added to calculate, as each species is added, how many base changes are the minimum which could be required at that site. The program runs fairly quickly. Usage Here is a sample session with fdnacomp % fdnacomp -ancseq -stepbox -printdata DNA compatibility algorithm Input (aligned) nucleotide sequence set(s): dnacomp.dat Phylip tree file (optional): Phylip weights file (optional): Phylip dnacomp program output file [dnacomp.fdnacomp]: Adding species: 1. Alpha 2. Beta 3. Gamma 4. Delta 5. Epsilon Doing global rearrangements !---------! ......... Output written to file "dnacomp.fdnacomp" Trees also written onto file "dnacomp.treefile" Go to the input files for this example Go to the output files for this example Example 2 % fdnacomp DNA compatibility algorithm Input (aligned) nucleotide sequence set(s): dnacomp.dat Phylip tree file (optional): dnacomptree.dat Phylip weights file (optional): Phylip dnacomp program output file [dnacomp.fdnacomp]: Output written to file "dnacomp.fdnacomp" Trees also written onto file "dnacomp.treefile" Go to the input files for this example Go to the output files for this example Command line arguments DNA compatibility algorithm Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-sequence] seqsetall File containing one or more sequence alignments [-intreefile] tree Phylip tree file (optional) -weights properties Phylip weights file (optional) [-outfile] outfile [*.fdnacomp] Phylip dnacomp program output file Additional (Optional) qualifiers (* if not always prompted): -outgrno integer [0] Species number to use as outgroup (Integer 0 or more) * -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) -[no]trout toggle [Y] Write out trees to tree file * -outtreefile outfile [*.fdnacomp] 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 -stepbox boolean [N] Print steps & compatibility at sites -ancseq boolean [N] Print sequences at all nodes of tree Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -scircular1 boolean Sequence is circular -squick1 boolean Read id and sequence only -sformat1 string Input sequence format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-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 fdnacomp reads any normal sequence USAs. Input files for usage example File: dnacomp.dat 5 13 Alpha AACGUGGCCAAAU Beta AAGGUCGCCAAAC Gamma CAUUUCGUCACAA Delta GGUAUUUCGGCCU Epsilon GGGAUCUCGGCCC Input files for usage example 2 File: dnacomptree.dat ((((Epsilon,Delta),Gamma),Beta),Alpha); Output file format fdnacomp output is standard: if option 1 is toggled on, the data is printed out, with the convention that "." means "the same as in the first species". Then comes a list of equally parsimonious trees, and (if option 2 is toggled on) a table of the number of changes of state required in each character. If option 5 is toggled on, a table is printed out after each tree, showing for each branch whether there are known to be changes in the branch, and what the states are inferred to have been at the top end of the branch. If the inferred state is a "?" or one of the IUB ambiguity symbols, there will be multiple equally-parsimonious assignments of states; the user must work these out for themselves by hand. A "?" in the reconstructed states means that in addition to one or more bases, a gap may or may not be present. If option 6 is left in its default state the trees found will be written to a tree file, so that they are available to be used in other programs. If the program finds multiple trees tied for best, all of these are written out onto the output tree file. Each is followed by a numerical weight in square brackets (such as [0.25000]). This is needed when we use the trees to make a consensus tree of the results of bootstrapping or jackknifing, to avoid overrepresenting replicates that find many tied trees. Output files for usage example File: dnacomp.fdnacomp DNA compatibility algorithm, version 3.69.650 5 species, 13 sites Name Sequences ---- --------- Alpha AACGTGGCCA AAT Beta AAGGTCGCCA AAC Gamma CATTTCGTCA CAA Delta GGTATTTCGG CCT Epsilon GGGATCTCGG CCC One most parsimonious tree found: +--Epsilon +--4 +--3 +--Delta ! ! +--2 +-----Gamma ! ! 1 +--------Beta ! +-----------Alpha remember: this is an unrooted tree! total number of compatible sites is 11.0 steps in each site: 0 1 2 3 4 5 6 7 8 9 *----------------------------------------- 0| 2 1 3 2 0 2 1 1 1 10| 1 1 1 3 compatibility (Y or N) of each site with this tree: 0123456789 *---------- 0 ! YYNYYYYYY 10 !YYYN From To Any Steps? State at upper node 1 AABGTSGCCA AAY 1 2 maybe AABGTCGCCA AAY 2 3 yes VAKDTCGCCA CAY 3 4 yes GGKATCTCGG CCY 4 Epsilon maybe GGGATCTCGG CCC 4 Delta yes GGTATTTCGG CCT 3 Gamma yes CATTTCGTCA CAA 2 Beta maybe AAGGTCGCCA AAC 1 Alpha maybe AACGTGGCCA AAT File: dnacomp.treefile ((((Epsilon,Delta),Gamma),Beta),Alpha); Output files for usage example 2 File: dnacomp.fdnacomp DNA compatibility algorithm, version 3.69.650 User-defined tree: +--Epsilon +--4 +--3 +--Delta ! ! +--2 +-----Gamma ! ! 1 +--------Beta ! +-----------Alpha remember: this is an unrooted tree! total number of compatible sites is 11.0 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 distmat Create a distance matrix from a multiple sequence alignment ednacomp DNA compatibility algorithm ednadist Nucleic acid sequence distance matrix program ednainvar Nucleic acid sequence invariants method ednaml Phylogenies from nucleic acid maximum likelihood ednamlk Phylogenies from nucleic acid maximum likelihood with clock ednapars DNA parsimony algorithm ednapenny Penny algorithm for DNA eprotdist Protein distance algorithm eprotpars Protein parsimony algorithm erestml Restriction site maximum likelihood method eseqboot Bootstrapped sequences algorithm fdiscboot Bootstrapped discrete sites algorithm fdnadist Nucleic acid sequence distance matrix program fdnainvar Nucleic acid sequence invariants method fdnaml Estimate nucleotide phylogeny by maximum likelihood fdnamlk Estimates nucleotide phylogeny by maximum likelihood fdnamove Interactive DNA parsimony fdnapars DNA parsimony algorithm fdnapenny Penny algorithm for DNA fdolmove Interactive Dollo or polymorphism parsimony ffreqboot Bootstrapped genetic frequencies algorithm fproml Protein phylogeny by maximum likelihood fpromlk Protein phylogeny by maximum likelihood fprotdist Protein distance algorithm fprotpars Protein parsimony algorithm frestboot Bootstrapped restriction sites algorithm frestdist Calculate distance matrix from restriction sites or fragments frestml Restriction site maximum likelihood method fseqboot Bootstrapped sequences algorithm fseqbootall Bootstrapped sequences algorithm 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