fdnacomp

 

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 sequence: dnacomp.dat
Input tree file: 
Weights file: 
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 sequence: dnacomp.dat
Input tree file: dnacomptree.dat
Weights file: 
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

   Standard (Mandatory) qualifiers:
  [-sequence]          seqsetall  File containing one or more sequence
                                  alignments
  [-intreefile]        tree       (no help text) tree value
   -weights            properties Weights file
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers (* if not always prompted):
   -outgrno            integer    Species number to use as outgroup
*  -njumble            integer    Number of times to randomise
*  -seed               integer    Random number seed between 1 and 32767 (must
                                  be odd)
   -[no]trout          toggle     Write out trees to tree file
*  -outtreefile        outfile    Tree file name
   -printdata          boolean    Print data at start of run
   -[no]progress       boolean    Print indications of progress of run
   -[no]treeprint      boolean    Print out tree
   -stepbox            boolean    Print steps & compatibility at sites
   -ancseq             boolean    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 standard output
   -filter             boolean    Read standard input, write 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. 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 deaths


Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)
File containing one or more sequence alignments Readable sets of sequences  
[-intreefile]
(Parameter 2)
(no help text) tree value Phylogenetic tree  
-weights Weights file Property value(s)  
[-outfile]
(Parameter 3)
Output file name Output file <sequence>.fdnacomp
Additional (Optional) qualifiers Allowed values Default
-outgrno Species number to use as outgroup Integer 0 or more 0
-njumble Number of times to randomise Integer 0 or more 0
-seed Random number seed between 1 and 32767 (must be odd) Integer from 1 to 32767 1
-[no]trout Write out trees to tree file Toggle value Yes/No Yes
-outtreefile Tree file name Output file  
-printdata Print data at start of run Boolean value Yes/No No
-[no]progress Print indications of progress of run Boolean value Yes/No Yes
-[no]treeprint Print out tree Boolean value Yes/No Yes
-stepbox Print steps & compatibility at sites Boolean value Yes/No No
-ancseq Print sequences at all nodes of tree Boolean value Yes/No No
Advanced (Unprompted) qualifiers Allowed values Default
(none)

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 3.6b

 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 3.6b

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 nameDescription
ednacompDNA compatibility algorithm
ednadistNucleic acid sequence Distance Matrix program
ednainvarNucleic acid sequence Invariants method
ednamlEstimates phylogenies from nucleic acid sequence Maximum Likelihood
ednamlkEstimates phylogenies from nucleic acid sequence Maximum Likelihood with molecular clock
ednaparsDNA parsimony algorithm
ednapennyPenny algorithm for DNA
eprotdistProtein distance algorithm
eprotparsProtein parsimony algorithm
erestmlRestriction site Maximum Likelihood method
eseqbootBootstrapped sequences algorithm
fdiscbootBootstrapped discrete sites algorithm
fdnadistNucleic acid sequence Distance Matrix program
fdnainvarNucleic acid sequence Invariants method
fdnamlEstimates nucleotide phylogeny by maximum likelihood
fdnamlkEstimates nucleotide phylogeny by maximum likelihood
fdnamoveInteractive DNA parsimony
fdnaparsDNA parsimony algorithm
fdnapennyPenny algorithm for DNA
fdolmoveInteractive Dollo or Polymorphism Parsimony
ffreqbootBootstrapped genetic frequencies algorithm
fpromlProtein phylogeny by maximum likelihood
fpromlkProtein phylogeny by maximum likelihood
fprotdistProtein distance algorithm
fprotparsProtein pasimony algorithm
frestbootBootstrapped restriction sites algorithm
frestdistComputes distance matrix from restriction sites or fragments
frestmlRestriction site maximum Likelihood method
fseqbootBootstrapped sequences algorithm
fseqbootallBootstrapped 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.