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fdnacomp |
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Function
DNA compatibility algorithmDescription
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:
- Each character evolves independently.
- Different lineages evolve independently.
- The ancestral base at each site is unknown.
- The rates of change in most sites over the time spans involved in the the divergence of the group are very small.
- A few of the sites have very high rates of change.
- 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:6.3.0
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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqsetall | File containing one or more sequence alignments | Readable sets of sequences | Required |
| [-intreefile] (Parameter 2) |
tree | Phylip tree file (optional) | Phylogenetic tree | |
| -weights | properties | Phylip weights file (optional) | Property value(s) | |
| [-outfile] (Parameter 3) |
outfile | Phylip dnacomp program output file | Output file | <*>.fdnacomp |
| Additional (Optional) qualifiers | ||||
| -outgrno | integer | Species number to use as outgroup | Integer 0 or more | 0 |
| -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 |
| -[no]trout | toggle | Write out trees to tree file | Toggle value Yes/No | Yes |
| -outtreefile | outfile | Phylip tree output file (optional) | Output file | <*>.fdnacomp |
| -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 |
| -stepbox | boolean | Print steps & compatibility at sites | Boolean value Yes/No | No |
| -ancseq | boolean | Print sequences at all nodes of tree | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqsetall qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-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
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
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 |
|---|---|
| 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.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.