                                    fpars



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

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
Phylip tree file (optional):
Phylip pars program 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

Discrete character parsimony
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            discretestates File containing one or more data sets
  [-intreefile]        tree       Phylip tree file (optional)
  [-outfile]           outfile    [*.fpars] Phylip pars program output file

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -method             menu       [Wagner] Choose the parsimony method to use
                                  (Values: w (Wagner); c (Camin-Sokal))
   -maxtrees           integer    [100] Number of trees to save (Integer from
                                  1 to 1000000)
*  -[no]thorough       toggle     [Y] More thorough search
*  -[no]rearrange      boolean    [Y] Rearrange on just one best tree
*  -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)
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -dothreshold        toggle     [N] Use threshold parsimony
*  -threshold          float      [1] Threshold value (Number 1.000 or more)
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.fpars] 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 at each site
   -ancseq             boolean    [N] Print states at all nodes of tree
*  -[no]dotdiff        boolean    [Y] 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 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


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 3.69.650


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
                    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

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 (c) 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.

Target users

                    This program is intended to be used by everyone and everything, from
                    naive users to embedded scripts.

Comments

None
