                                  fdnacomp



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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:6.2.0

   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
   -sformat1           string     Input sequence format
   -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

 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

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       Estimates 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    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.

                    Although we take every care to ensure that the results of the EMBOSS
                    version are identical to those from the original package, we recommend
                    that you check your inputs give the same results in both versions
                    before publication.

                    Please report all bugs in the EMBOSS version to the EMBOSS bug team,
                    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.
