fdolpenny

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Function

Description

Algorithm

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 Algorithm

The search strategy used by DOLPENNY 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 losses. 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.

Actually 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. Its 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 bifurcating 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 losses (or retentions of polymorphism) is evaluated.

The point of this is that if a previously-found tree such as ((A,B),(C,D)) required fewer losses, 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.

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 the list 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.

Controlling Run Times

Among the quantities available to be set at the beginning of a run of DOLPENNY, two (howoften and howmany) are of particular importance. As DOLPENNY goes along it will keep count of how many trees it has examined. Suppose that howoften is 100 and howmany is 300, the default settings. Every time 100 trees have been examined, DOLPENNY will print out a line saying how many multiples of 100 trees have now been examined, how many steps the most parsimonious tree found so far has, how many trees of with that number of steps have been found, and a very rough estimate of what fraction of all trees have been looked at so far.

When the number of these multiples printed out reaches the number howmany (say 1000), the whole algorithm aborts and prints out that it has not found all most parsimonious trees, but prints out what is has got so far anyway. These trees need not be any of the most parsimonious trees: they are simply the most parsimonious ones found so far. By setting the product (howoften X howmany) large you can make the algorithm less likely to abort, but then you risk getting bogged down in a gigantic computation. You should adjust these constants so that the program cannot go beyond examining the number of trees you are reasonably willing to pay for (or wait for). In their initial setting the program will abort after looking at 100,000 trees. Obviously you may want to adjust howoften in order to get more or fewer lines of intermediate notice of how many trees have been looked at so far. Of course, in small cases you may never even reach the first multiple of howoften and nothing will be printed out except some headings and then the final trees.

The indication of the approximate percentage of trees searched so far will be helpful in judging how much farther you would have to go to get the full search. Actually, since that fraction is the fraction of the set of all possible trees searched or ruled out so far, and since the search becomes progressively more efficient, the approximate fraction printed out will usually be an underestimate of how far along the program is, sometimes a serious underestimate.

A constant 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.

Methods and Options

The counting of the length of trees is done by an algorithm nearly identical to the corresponding algorithms in DOLLOP, and thus the remainder of this document will be nearly identical to the DOLLOP document. The Dollo parsimony method was first suggested in print in verbal form by Le Quesne (1974) and was first well-specified by Farris (1977). The method is named after Louis Dollo since he was one of the first to assert that in evolution it is harder to gain a complex feature than to lose it. The algorithm explains the presence of the state 1 by allowing up to one forward change 0-->1 and as many reversions 1-->0 as are necessary to explain the pattern of states seen. The program attempts to minimize the number of 1-->0 reversions necessary.

The assumptions of this method are in effect:

1. We know which state is the ancestral one (state 0).
2. The characters are evolving independently.
3. Different lineages evolve independently.
4. The probability of a forward change (0-->1) is small over the evolutionary times involved.
5. The probability of a reversion (1-->0) is also small, but still far larger than the probability of a forward change, so that many reversions are easier to envisage than even one extra forward change.
6. Retention of polymorphism for both states (0 and 1) is highly improbable.
7. The lengths of the segments of the true tree are not so unequal that two changes in a long segment are as probable as one in a short segment.

That these are the assumptions is established in several of my papers (1973a, 1978b, 1979, 1981b, 1983). 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).

One problem can arise when using additive binary recoding to represent a multistate character as a series of two-state characters. Unlike the Camin-Sokal, Wagner, and Polymorphism methods, the Dollo method can reconstruct ancestral states which do not exist. An example is given in my 1979 paper. It will be necessary to check the output to make sure that this has not occurred.

The polymorphism parsimony method was first used by me, and the results published (without a clear specification of the method) by Inger (1967). The method was published by Farris (1978a) and by me (1979). The method assumes that we can explain the pattern of states by no more than one origination (0-->1) of state 1, followed by retention of polymorphism along as many segments of the tree as are necessary, followed by loss of state 0 or of state 1 where necessary. The program tries to minimize the total number of polymorphic characters, where each polymorphism is counted once for each segment of the tree in which it is retained.

The assumptions of the polymorphism parsimony method are in effect:

1. The ancestral state (state 0) is known in each character.
2. The characters are evolving independently of each other.
3. Different lineages are evolving independently.
4. Forward change (0-->1) is highly improbable over the length of time involved in the evolution of the group.
5. Retention of polymorphism is also improbable, but far more probable that forward change, so that we can more easily envisage much polymorhism than even one additional forward change.
6. Once state 1 is reached, reoccurrence of state 0 is very improbable, much less probable than multiple retentions of polymorphism.
7. The lengths of segments in the true tree are not so unequal that we can more easily envisage retention events occurring in both of two long segments than one retention in a short segment.

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).

Usage

% fdolpenny Penny algorithm Dollo or polymorphism Phylip character discrete states file: dolpenny.dat Phylip dolpenny program output file [dolpenny.fdolpenny]: How many trees looked Approximate at so far Length of How many percentage (multiples shortest tree trees this long searched of 100): found so far found so far so far ---------- ------------ ------------ ------------ 1 3.00000 1 0.95 Output written to file "dolpenny.fdolpenny" Trees also written onto file "dolpenny.treefile"

Go to the input files for this example
Go to the output files for this example

Command line arguments

Penny algorithm Dollo or polymorphism
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            discretestates File containing one or more data sets
  [-outfile]           outfile    [*.fdolpenny] Phylip dolpenny program output
                                  file

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -ancfile            properties Ancestral states file
   -dothreshold        toggle     [N] Use threshold parsimony
*  -threshold          float      [1] Threshold value (Number 0.000 or more)
   -howmany            integer    [1000] How many groups of trees (Any integer
                                  value)
   -howoften           integer    [100] How often to report, in trees (Any
                                  integer value)
   -[no]simple         boolean    [Y] Branch and bound is simple
   -method             menu       [d] Parsimony method (Values: d (Dollo); p
                                  (Polymorphism))
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.fdolpenny] 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
   -ancseq             boolean    [N] Print states at all nodes of tree
   -stepbox            boolean    [N] Print out steps in each character

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-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
[-infile] (Parameter 1)	discretestates	File containing one or more data sets	Discrete states file
[-outfile] (Parameter 2)	outfile	Phylip dolpenny program output file	Output file	<*>.fdolpenny
Additional (Optional) qualifiers
-weights	properties	Weights file	Property value(s)
-ancfile	properties	Ancestral states file	Property value(s)
-dothreshold	toggle	Use threshold parsimony	Toggle value Yes/No	No
-threshold	float	Threshold value	Number 0.000 or more	1
-howmany	integer	How many groups of trees	Any integer value	1000
-howoften	integer	How often to report, in trees	Any integer value	100
-[no]simple	boolean	Branch and bound is simple	Boolean value Yes/No	Yes
-method	list	Parsimony method	d (Dollo) p (Polymorphism)	d
-[no]trout	toggle	Write out trees to tree file	Toggle value Yes/No	Yes
-outtreefile	outfile	Phylip tree output file (optional)	Output file	<*>.fdolpenny
-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
-ancseq	boolean	Print states at all nodes of tree	Boolean value Yes/No	No
-stepbox	boolean	Print out steps in each character	Boolean value Yes/No	No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-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

Input file format

(0,1) Discrete character data

These programs are intended for the use of morphological systematists who are dealing with discrete characters, or by molecular evolutionists dealing with presence-absence data on restriction sites. One of the programs (PARS) allows multistate characters, with up to 8 states, plus the unknown state symbol "?". For the others, the characters are assumed to be coded into a series of (0,1) two-state characters. For most of the programs there are two other states possible, "P", which stands for the state of Polymorphism for both states (0 and 1), and "?", which stands for the state of ignorance: it is the state "unknown", or "does not apply". The state "P" can also be denoted by "B", for "both".

There is a method invented by Sokal and Sneath (1963) for linear sequences of character states, and fully developed for branching sequences of character states by Kluge and Farris (1969) for recoding a multistate character into a series of two-state (0,1) characters. Suppose we had a character with four states whose character-state tree had the rooted form:

               1 ---> 0 ---> 2
                      |
                      |
                      V
                      3

so that 1 is the ancestral state and 0, 2 and 3 derived states. We can represent this as three two-state characters:

                Old State           New States
                --- -----           --- ------
                    0                  001
                    1                  000
                    2                  011
                    3                  101

The three new states correspond to the three arrows in the above character state tree. Possession of one of the new states corresponds to whether or not the old state had that arrow in its ancestry. Thus the first new state corresponds to the bottommost arrow, which only state 3 has in its ancestry, the second state to the rightmost of the top arrows, and the third state to the leftmost top arrow. This coding will guarantee that the number of times that states arise on the tree (in programs MIX, MOVE, PENNY and BOOT) or the number of polymorphic states in a tree segment (in the Polymorphism option of DOLLOP, DOLMOVE, DOLPENNY and DOLBOOT) will correctly correspond to what would have been the case had our programs been able to take multistate characters into account. Although I have shown the above character state tree as rooted, the recoding method works equally well on unrooted multistate characters as long as the connections between the states are known and contain no loops.

However, in the default option of programs DOLLOP, DOLMOVE, DOLPENNY and DOLBOOT the multistate recoding does not necessarily work properly, as it may lead the program to reconstruct nonexistent state combinations such as 010. An example of this problem is given in my paper on alternative phylogenetic methods (1979).

If you have multistate character data where the states are connected in a branching "character state tree" you may want to do the binary recoding yourself. Thanks to Christopher Meacham, the package contains a program, FACTOR, which will do the recoding itself. For details see the documentation file for FACTOR.

We now also have the program PARS, which can do parsimony for unordered character states.

Input files for usage example

File: dolpenny.dat

    7    6
Alpha1    110110
Alpha2    110110
Beta1     110000
Beta2     110000
Gamma1    100110
Delta     001001
Epsilon   001110

Output file format

A table is available to be 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 "?" there will be multiple equally-parsimonious assignments of states; the user must work these out for themselves by hand.

If the A option is used, then the program will infer, for any character whose ancestral state is unknown ("?") whether the ancestral state 0 or 1 will give the best tree. If these are tied, then it may not be possible for the program to infer the state in the internal nodes, and these will all be printed as ".". If this has happened and you want to know more about the states at the internal nodes, you will find helpful to use DOLMOVE to display the tree and examine its interior states, as the algorithm in DOLMOVE shows all that can be known in this case about the interior states, including where there is and is not amibiguity. The algorithm in DOLPENNY gives up more easily on displaying these states.

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: dolpenny.fdolpenny

Penny algorithm for Dollo or polymorphism parsimony, version 3.69.650
 branch-and-bound to find all most parsimonious trees


requires a total of              3.000

    3 trees in all found




  +-----------------Delta     
  !  
--2  +--------------Epsilon   
  !  !  
  +--3  +-----------Gamma1    
     !  !  
     +--6  +--------Alpha2    
        !  !  
        +--1     +--Beta2     
           !  +--5  
           +--4  +--Beta1     
              !  
              +-----Alpha1    





  +-----------------Delta     
  !  
--2  +--------------Epsilon   
  !  !  
  +--3  +-----------Gamma1    
     !  !  
     +--6        +--Beta2     
        !  +-----5  
        !  !     +--Beta1     
        +--4  
           !     +--Alpha2    
           +-----1  
                 +--Alpha1    





  +-----------------Delta     
  !  
--2  +--------------Epsilon   
  !  !  
  +--3  +-----------Gamma1    
     !  !  
     !  !        +--Beta2     
     +--6     +--5  
        !  +--4  +--Beta1     
        !  !  !  
        +--1  +-----Alpha2    
           !  
           +--------Alpha1    

File: dolpenny.treefile

(Delta,(Epsilon,(Gamma1,(Alpha2,((Beta2,Beta1),Alpha1)))))[0.3333];
(Delta,(Epsilon,(Gamma1,((Beta2,Beta1),(Alpha2,Alpha1)))))[0.3333];
(Delta,(Epsilon,(Gamma1,(((Beta2,Beta1),Alpha2),Alpha1))))[0.3333];

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users

Comments

None