
                                   fpars 



Function

   Discrete character parsimony

Description

   Multistate discrete-characters parsimony method. Up to 8 states (as
   well as "?") are allowed. Cannot do Camin-Sokal or Dollo Parsimony.
   Can cope with multifurcations, reconstruct ancestral states, use
   character weights, and infer branch lengths.

Algorithm

   PARS is a general parsimony program which carries out the Wagner
   parsimony method with multiple states. Wagner parsimony allows changes
   among all states. The criterion is to find the tree which requires the
   minimum number of changes. The Wagner method was originated by Eck and
   Dayhoff (1966) and by Kluge and Farris (1969). Here are its
   assumptions:
    1. Ancestral states are unknown unknown.
    2. Different characters evolve independently.
    3. Different lineages evolve independently.
    4. Changes to all other states are equally probable (Wagner).
    5. These changes are a priori improbable over the evolutionary time
       spans involved in the differentiation of the group in question.
    6. Other kinds of evolutionary event such as retention of
       polymorphism are far less probable than these state changes.
    7. Rates of evolution in different lineages are sufficiently low that
       two changes in a long segment of the tree are far less probable
       than one change 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

   Here is a sample session with fpars


% fpars 
Discrete character parsimony
Input file: pars.dat
Input tree file: 
Output file [pars.fpars]: 

Adding species:
   1. Alpha
   2. Beta
   3. Gamma
   4. Delta
   5. Epsilon

Doing global rearrangements on the first of the trees tied for best
  !---------!
   .........
   .........

Collapsing best trees
   .

Output written to file "pars.fpars"

Tree also written onto file "pars.treefile"

Done.


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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infile]            discretestates File containing one or more data sets
  [-intreefile]        tree       (no help text) tree value
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -method             menu       Choose the parsimony method to use
   -maxtrees           integer    Number of trees to save
*  -[no]thorough       toggle     More thorough search
*  -[no]rearrange      boolean    Rearrange on just one best tree
*  -njumble            integer    Number of times to randomise
*  -seed               integer    Random number seed between 1 and 32767 (must
                                  be odd)
   -outgrno            integer    Species number to use as outgroup
   -thresh             toggle     Use threshold parsimony
*  -threshold          float      Threshold value
   -[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 at each site
   -ancseq             boolean    Print states at all nodes of tree
*  -[no]dotdiff        boolean    Use dot differencing to display results

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

   "-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
   [-infile]
   (Parameter 1) File containing one or more data sets Discrete states
   file
   [-intreefile]
   (Parameter 2) (no help text) tree value Phylogenetic tree
   [-outfile]
   (Parameter 3) Output file name Output file <sequence>.fpars
   Additional (Optional) qualifiers Allowed values Default
   -weights Weights file Property value(s)
   -method Choose the parsimony method to use
   w (Wagner)
   c (Camin-Sokal)
   Wagner
   -maxtrees Number of trees to save Integer from 1 to 1000000 100
   -[no]thorough More thorough search Toggle value Yes/No Yes
   -[no]rearrange Rearrange on just one best tree Boolean value Yes/No
   Yes
   -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
   -outgrno Species number to use as outgroup Integer 0 or more 0
   -thresh Use threshold parsimony Toggle value Yes/No No
   -threshold Threshold value Number 1.000 or more 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 at each site Boolean value Yes/No No
   -ancseq Print states at all nodes of tree Boolean value Yes/No No
   -[no]dotdiff Use dot differencing to display results Boolean value
   Yes/No Yes
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   fpars reads discrete characters input, except that multiple states (up
   to 9 of them) are allowed. Any characters other than "?" are allowed
   as states, up to a maximum of 9 states. In fact, one can use different
   symbols in different columns of the data matrix, although it is rather
   unlikely that you would want to do that. The symbols you can use are:
     * The digits 0-9,
     * The letters A-Z and a-z,
     * The symbols "!\"#$%&'()*+,-./:;<=>?@\[\\]^_`\{|}~
       (of these, probably only + and - will be of interest to most
       users).

   But note that these do not include blank (" "). Blanks in the input
   data are simply skipped by the program, so that they can be used to
   make characters into groups for ease of viewing. The "?" (question
   mark) symbol has special meaning. It is allowed in the input but is
   not available as the symbol of a state. Rather, it means that the
   state is unknown.

   PARS can handle both bifurcating and multifurcating trees. In doing
   its search for most parsimonious trees, it adds species not only by
   creating new forks in the middle of existing branches, but it also
   tries putting them at the end of new branches which are added to
   existing forks. Thus it searches among both bifurcating and
   multifurcating trees. If a branch in a tree does not have any
   characters which might change in that branch in the most parsimonious
   tree, it does not save that tree. Thus in any tree that results, a
   branch exists only if some character has a most parsimonious
   reconstruction that would involve change in that branch.

   It also saves a number of trees tied for best (you can alter the
   number it saves using the V option in the menu). When rearranging
   trees, it tries rearrangements of all of the saved trees. This makes
   the algorithm slower than earlier programs such as MIX.

  (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: pars.dat

     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110

Output file format

   fpars 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. Each
   tree has branch lengths. These are computed using an algorithm
   published by Hochbaum and Pathria (1997) which I first heard of from
   Wayne Maddison who invented it independently of them. This algorithm
   averages the number of reconstructed changes of state over all sites a
   over all possible most parsimonious placements of the changes of state
   among branches. Note that it does not correct in any way for multiple
   changes that overlay each other.

   If option 2 is toggled on a table of the number of changes of state
   required in each character is also printed. 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. This is
   a reconstruction of the ancestral sequences in the tree. If you choose
   option 5, a menu item D appears which gives you the opportunity to
   turn off dot-differencing so that complete ancestral sequences are
   shown. 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 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.

   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 best tree. This test, which is a version of
   the test proposed by Alan Templeton (1983) and evaluated in a test
   case by me (1985a). It is closely parallel to a test using log
   likelihood differences due to Kishino and Hasegawa (1989), and uses
   the mean and variance of step differences between trees, taken across
   sites. If the mean is more than 1.96 standard deviations different
   then the trees are declared significantly different. The program
   prints out a table of the steps for each tree, the differences of each
   from the best one, the variance of that quantity as determined by the
   step differences at individual sites, and a conclusion as to whether
   that tree is or is not significantly worse than the best one. It is
   important to understand that the test assumes that all the discrete
   characters are evolving independently, which is unlikely to be true
   for

   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 sums of steps across
   characters 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 number of steps,
   numbers of steps 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 lowest number of steps 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
   number of steps for each tree, the differences of each from the lowest
   one, the variance of that quantity as determined by the differences of
   the numbers of steps at individual characters, and a conclusion as to
   whether that tree is or is not significantly worse than the best one.

   Option 6 in the menu controls whether the tree estimated by the
   program is written onto a tree file. The default name of this output
   tree file is "outtree". If the U option is in effect, all the
   user-defined trees are written to the output tree file.

  Output files for usage example

  File: pars.fpars


Discrete character parsimony algorithm, version 3.6b


One most parsimonious tree found:


                            +Epsilon
           +----------------3
  +--------2                +-------------------------Delta
  |        |
  |        +Gamma
  |
  1----------------Beta
  |
  +Alpha


requires a total of      8.000

  between      and       length
  -------      ---       ------
     1           2         1.00
     2           3         2.00
     3      Epsilon        0.00
     3      Delta          3.00
     2      Gamma          0.00
     1      Beta           2.00
     1      Alpha          0.00

  File: pars.treefile

   (((Epsilon:0.00,Delta:3.00):2.00,Gamma:0.00):1.00,Beta:2.00,Alpha:0.00);

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
   eclique Largest clique program
   edollop Dollo and polymorphism parsimony algorithm
   edolpenny Penny algorithm Dollo or polymorphism
   efactor Multistate to binary recoding program
   emix Mixed parsimony algorithm
   epenny Penny algorithm, branch-and-bound to find all most parsimonious
   trees
   fclique Largest clique program
   fdollop Dollo and polymorphism parsimony algorithm
   fdolpenny Penny algorithm Dollo or polymorphism
   ffactor Multistate to binary recoding program
   fmix Mixed parsimony algorithm
   fmove Interactive mixed method parsimony
   fpenny Penny algorithm, branch-and-bound to find all most parsimonious
   trees

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.
