fdnapenny |
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DNAPENNY is a program that will find all of the most parsimonious trees implied by your data when the nucleic acid sequence parsimony criterion is employed. It does so not by examining all possible trees, but by using the more sophisticated "branch and bound" algorithm, a standard computer science search strategy first applied to phylogenetic inference by Hendy and Penny (1982). (J. S. Farris [personal communication, 1975] had also suggested that this strategy, which is well-known in computer science, might be applied to phylogenies, but he did not publish this suggestion).
There is, however, a price to be paid for the certainty that one has found all members of the set of most parsimonious trees. The problem of finding these has been shown (Graham and Foulds, 1982; Day, 1983) to be NP-complete, which is equivalent to saying that there is no fast algorithm that is guaranteed to solve the problem in all cases (for a discussion of NP-completeness, see the Scientific American article by Lewis and Papadimitriou, 1978). The result is that this program, despite its algorithmic sophistication, is VERY SLOW.
The program should be slower than the other tree-building programs in the package, but useable up to about ten species. Above this it will bog down rapidly, but exactly when depends on the data and on how much computer time you have (it may be more effective in the hands of someone who can let a microcomputer grind all night than for someone who has the "benefit" of paying for time on the campus mainframe computer). IT IS VERY IMPORTANT FOR YOU TO GET A FEEL FOR HOW LONG THE PROGRAM WILL TAKE ON YOUR DATA. This can be done by running it on subsets of the species, increasing the number of species in the run until you either are able to treat the full data set or know that the program will take unacceptably long on it. (Making a plot of the logarithm of run time against species number may help to project run times).
The search strategy used by DNAPENNY starts by making a tree consisting of the first two species (the first three if the tree is to be unrooted). Then it tries to add the next species in all possible places (there are three of these). For each of the resulting trees it evaluates the number of base substitutions. It adds the next species to each of these, again in all possible spaces. If this process would continue it would simply generate all possible trees, of which there are a very large number even when the number of species is moderate (34,459,425 with 10 species). Actually it does not do this, because the trees are generated in a particular order and some of them are never generated.
This is because the order in which trees are generated is not quite as implied above, but is a "depth-first search". This means that first one adds the third species in the first possible place, then the fourth species in its first possible place, then the fifth and so on until the first possible tree has been produced. For each tree the number of steps is evaluated. Then one "backtracks" by trying the alternative placements of the last species. When these are exhausted one tries the next placement of the next-to-last species. The order of placement in a depth-first search is like this for a four-species case (parentheses enclose monophyletic groups):
Make tree of first two species: (A,B) Add C in first place: ((A,B),C) Add D in first place: (((A,D),B),C) Add D in second place: ((A,(B,D)),C) Add D in third place: (((A,B),D),C) Add D in fourth place: ((A,B),(C,D)) Add D in fifth place: (((A,B),C),D) Add C in second place: ((A,C),B) Add D in first place: (((A,D),C),B) Add D in second place: ((A,(C,D)),B) Add D in third place: (((A,C),D),B) Add D in fourth place: ((A,C),(B,D)) Add D in fifth place: (((A,C),B),D) Add C in third place: (A,(B,C)) Add D in first place: ((A,D),(B,C)) Add D in second place: (A,((B,D),C)) Add D in third place: (A,(B,(C,D))) Add D in fourth place: (A,((B,C),D)) Add D in fifth place: ((A,(B,C)),D)
Among these fifteen trees you will find all of the four-species rooted trees, each exactly once (the parentheses each enclose a monophyletic group). As displayed above, the backtracking depth-first search algorithm is just another way of producing all possible trees one at a time. The branch and bound algorithm consists of this with one change. As each tree is constructed, including the partial trees such as (A,(B,C)), its number of steps is evaluated. In addition a prediction is made as to how many steps will be added, at a minimum, as further species are added.
This is done by counting how many sites which are invariant in the data up the most recent species added will ultimately show variation when further species are added. Thus if 20 sites vary among species A, B, and C and their root, and if tree ((A,C),B) requires 24 steps, then if there are 8 more sites which will be seen to vary when species D is added, we can immediately say that no matter how we add D, the resulting tree can have no less than 24 + 8 = 32 steps. The point of all this is that if a previously-found tree such as ((A,B),(C,D)) required only 30 steps, then we know that there is no point in even trying to add D to ((A,C),B). We have computed the bound that enables us to cut off a whole line of inquiry (in this case five trees) and avoid going down that particular branch any farther.
The branch-and-bound algorithm thus allows us to find all most parsimonious trees without generating all possible trees. How much of a saving this is depends strongly on the data. For very clean (nearly "Hennigian") data, it saves much time, but on very messy data it will still take a very long time.
The algorithm in the program differs from the one outlined here in some essential details: it investigates possibilities in the order of their apparent promise. This applies to the order of addition of species, and to the places where they are added to the tree. After the first two-species tree is constructed, the program tries adding each of the remaining species in turn, each in the best possible place it can find. Whichever of those species adds (at a minimum) the most additional steps is taken to be the one to be added next to the tree. When it is added, it is added in turn to places which cause the fewest additional steps to be added. This sounds a bit complex, but it is done with the intention of eliminating regions of the search of all possible trees as soon as possible, and lowering the bound on tree length as quickly as possible. This process of evaluating which species to add in which order goes on the first time the search makes a tree; thereafter it uses that order.
The program keeps a list of all the most parsimonious trees found so far. Whenever it finds one that has fewer losses than these, it clears out the list and restarts it with that tree. In the process the bound tightens and fewer possibilities need be investigated. At the end the list contains all the shortest trees. These are then printed out. It should be mentioned that the program CLIQUE for finding all largest cliques also works by branch-and-bound. Both problems are NP-complete but for some reason CLIQUE runs far faster. Although their worst-case behavior is bad for both programs, those worst cases occur far more frequently in parsimony problems than in compatibility problems.
A constant at the beginning of the program that affects the result is "maxtrees", which controls the maximum number of trees that can be stored. Thus if maxtrees is 25, and 32 most parsimonious trees are found, only the first 25 of these are stored and printed out. If maxtrees is increased, the program does not run any slower but requires a little more intermediate storage space. I recommend that maxtrees be kept as large as you can, provided you are willing to look at an output with that many trees on it! Initially, maxtrees is set to 100 in the distribution copy.
This program carries out unrooted parsimony (analogous to Wagner trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA sequences. The method of Fitch (1971) is used to count the number of changes of base needed on a given tree. The assumptions of this method are exactly analogous to those of DNAPARS:
Change from an occupied site to a deletion is counted as one change. Reversion from a deletion to an occupied site is allowed and is also counted as one change. That these are the assumptions of parsimony methods has been documented in a series of papers of mine: (1973a, 1978b, 1979, 1981b, 1983b, 1988b). For an opposing view arguing that the parsimony methods make no substantive assumptions such as these, see the papers by Farris (1983) and Sober (1983a, 1983b), but also read the exchange between Felsenstein and Sober (1986). Change from an occupied site to a deletion is counted as one change. Reversion from a deletion to an occupied site is allowed and is also counted as one change. Note that this in effect assumes that a deletion N bases long is N separate events.
% fdnapenny Penny algorithm for DNA Input (aligned) nucleotide sequence set(s): dnapenny.dat Phylip dnapenny program output file [dnapenny.fdnapenny]: justweights: false numwts: 0 How many trees looked Approximate at so far Length of How many percentage (multiples shortest tree trees this short searched of 100): found so far found so far so far ---------- ------------ ------------ ------------ 1 9.0 2 0.11 2 8.0 3 6.67 3 8.0 9 20.00 4 8.0 9 86.67 Output written to file "dnapenny.fdnapenny" Trees also written onto file "dnapenny.treefile" |
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Penny algorithm for DNA Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqsetall File containing one or more sequence alignments [-outfile] outfile [*.fdnapenny] Phylip dnapenny program output file Additional (Optional) qualifiers (* if not always prompted): -weights properties (no help text) properties value -howoften integer [100] How often to report, in trees (Any integer value) -howmany integer [1000] How many groups of trees (Any integer value) -[no]simple boolean [Y] Branch and bound is simple -outgrno integer [0] Species number to use as outgroup (Integer 0 or more) -thresh toggle [N] Use threshold parsimony * -threshold float [1.0] Threshold value (Number 1.000 or more) -[no]trout toggle [Y] Write out trees to tree file * -outtreefile outfile [*.fdnapenny] 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 out steps in each site -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 -odirectory2 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 |
[-outfile] (Parameter 2) |
outfile | Phylip dnapenny program output file | Output file | <*>.fdnapenny |
Additional (Optional) qualifiers | ||||
-weights | properties | (no help text) properties value | Property value(s) | |
-howoften | integer | How often to report, in trees | Any integer value | 100 |
-howmany | integer | How many groups of trees | Any integer value | 1000 |
-[no]simple | boolean | Branch and bound is simple | Boolean value Yes/No | Yes |
-outgrno | integer | Species number to use as outgroup | Integer 0 or more | 0 |
-thresh | toggle | Use threshold parsimony | Toggle value Yes/No | No |
-threshold | float | Threshold value | Number 1.000 or more | 1.0 |
-[no]trout | toggle | Write out trees to tree file | Toggle value Yes/No | Yes |
-outtreefile | outfile | Phylip tree output file (optional) | Output file | <*>.fdnapenny |
-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 out steps in each site | 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 | ||||
-odirectory2 -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 |
8 6 Alpha1 AAGAAG Alpha2 AAGAAG Beta1 AAGGGG Beta2 AAGGGG Gamma1 AGGAAG Gamma2 AGGAAG Delta GGAGGA Epsilon GGAAAG |
Penny algorithm for DNA, version 3.69 branch-and-bound to find all most parsimonious trees requires a total of 8.000 9 trees in all found +--------------------Alpha1 ! ! +-----------Alpha2 ! ! 1 +-----4 +--Epsilon ! ! ! +-----6 ! ! ! ! +--Delta ! ! +--5 +--2 ! +--Gamma2 ! +-----7 ! +--Gamma1 ! ! +--Beta2 +--------------3 +--Beta1 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +-----------Alpha2 ! ! 1 +-----4 +--------Gamma2 ! ! ! ! ! ! +--7 +--Epsilon ! ! ! +--6 +--2 +--5 +--Delta ! ! ! +-----Gamma1 ! ! +--Beta2 +--------------3 +--Beta1 [Part of this file has been deleted for brevity] +--5 +--Delta ! +-----Gamma1 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +-----Alpha2 1 +-----------2 ! ! ! +--Beta2 ! ! +--3 ! ! +--Beta1 +--4 ! +-----Gamma2 ! +--7 ! ! ! +--Epsilon +--------5 +--6 ! +--Delta ! +--------Gamma1 remember: this is an unrooted tree! +--------------------Alpha1 ! ! +-----Alpha2 1 +-----------2 ! ! ! +--Beta2 ! ! +--3 ! ! +--Beta1 +--4 ! +--Epsilon ! +-----6 ! ! +--Delta +--------5 ! +--Gamma2 +-----7 +--Gamma1 remember: this is an unrooted tree! |
(Alpha1,((Alpha2,((Epsilon,Delta),(Gamma2,Gamma1))),(Beta2,Beta1)))[0.1111]; (Alpha1,((Alpha2,(Gamma2,((Epsilon,Delta),Gamma1))),(Beta2,Beta1)))[0.1111]; (Alpha1,((Alpha2,((Gamma2,(Epsilon,Delta)),Gamma1)),(Beta2,Beta1)))[0.1111]; (Alpha1,(Alpha2,((Gamma2,((Epsilon,Delta),Gamma1)),(Beta2,Beta1))))[0.1111]; (Alpha1,(Alpha2,(((Epsilon,Delta),(Gamma2,Gamma1)),(Beta2,Beta1))))[0.1111]; (Alpha1,(Alpha2,(((Gamma2,(Epsilon,Delta)),Gamma1),(Beta2,Beta1))))[0.1111]; (Alpha1,((Alpha2,(Beta2,Beta1)),(Gamma2,((Epsilon,Delta),Gamma1))))[0.1111]; (Alpha1,((Alpha2,(Beta2,Beta1)),((Gamma2,(Epsilon,Delta)),Gamma1)))[0.1111]; (Alpha1,((Alpha2,(Beta2,Beta1)),((Epsilon,Delta),(Gamma2,Gamma1))))[0.1111]; |
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 |
fdnacomp | DNA compatibility 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 |
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.