                                    fmix



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Function

   Mixed parsimony algorithm

Description

   Estimates phylogenies by some parsimony methods for discrete character
   data with two states (0 and 1). Allows use of the Wagner parsimony
   method, the Camin-Sokal parsimony method, or arbitrary mixtures of
   these. Also reconstructs ancestral states and allows weighting of
   characters (does not infer branch lengths).

Algorithm

   MIX is a general parsimony program which carries out the Wagner and
   Camin-Sokal parsimony methods in mixture, where each character can have
   its method specified separately. The program defaults to carrying out
   Wagner parsimony.

   The Camin-Sokal parsimony method explains the data by assuming that
   changes 0 --> 1 are allowed but not changes 1 --> 0. Wagner parsimony
   allows both kinds of changes. (This under the assumption that 0 is the
   ancestral state, though the program allows reassignment of the
   ancestral state, in which case we must reverse the state numbers 0 and
   1 throughout this discussion). The criterion is to find the tree which
   requires the minimum number of changes. The Camin-Sokal method is due
   to Camin and Sokal (1965) and the Wagner method to Eck and Dayhoff
   (1966) and to Kluge and Farris (1969).

   Here are the assumptions of these two methods:
    1. Ancestral states are known (Camin-Sokal) or unknown (Wagner).
    2. Different characters evolve independently.
    3. Different lineages evolve independently.
    4. Changes 0 --> 1 are much more probable than changes 1 --> 0
       (Camin-Sokal) or equally probable (Wagner).
    5. Both of these kinds of 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 0 --> 1 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 fmix


% fmix
Mixed parsimony algorithm
Phylip character discrete states file: mix.dat
Phylip tree file (optional):
Phylip mix program output file [mix.fmix]:

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

Doing global rearrangements
  !---------!
   .........


Output written to file "mix.fmix"

Trees also written onto file "mix.treefile"



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

   Example 2


% fmix -printdata -ancfile mixancfile.dat
Mixed parsimony algorithm
Phylip character discrete states file: mix.dat
Phylip tree file (optional):
Phylip mix program output file [mix.fmix]:

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

Doing global rearrangements
  !---------!
   .........


Output written to file "mix.fmix"

Trees also written onto file "mix.treefile"



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

Command line arguments

Mixed parsimony algorithm
Version: EMBOSS:6.2.0

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

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -ancfile            properties Ancestral states file
   -mixfile            properties Mixture file
   -method             menu       [Wagner] Choose the method to use (Values: w
                                  (Wagner); c (Camin-Sokal); m (Mixed))
*  -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)
   -threshold          float      [$(infile.discretesize)] Threshold value
                                  (Number 1.000 or more)
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.fmix] 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
   -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

   fmix reads discrete character data. States "?", "P", and "B" are
   allowed.

  (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: mix.dat

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

  Input files for usage example 2

  File: mixancfile.dat

001??1

Output file format

   fmix output is standard: a list of equally parsimonious trees, which
   will be printed as rooted or unrooted depending on which is
   appropriate, and, if the user chooses, a table of the number of changes
   of state required in each character. If the Wagner option is in force
   for a character, it may not be possible to unambiguously locate the
   places on the tree where the changes occur, as there may be multiple
   possibilities. If the user selects menu option 5, 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 "?" there will
   be multiple equally-parsimonious assignments of states; the user must
   work these out for themselves by hand.

   If the Camin-Sokal parsimony method is invoked and the Ancestors option
   is also used, then the program will infer, for any character whose
   ancestral state is unknown ("?") whether the ancestral state 0 or 1
   will give the fewest state changes. 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 MOVE to display the tree and examine its interior
   states, as the algorithm in MOVE shows all that can be known in this
   case about the interior states, including where there is and is not
   amibiguity. The algorithm in MIX gives up more easily on displaying
   these states.

   If the A option is not used, then the program will assume 0 as the
   ancestral state for those characters following the Camin-Sokal method,
   and will assume that the ancestral state is unknown for those
   characters following Wagner parsimony. If any characters have unknown
   ancestral states, and if the resulting tree is rooted (even by
   outgroup), a table will also be printed out showing the best guesses of
   which are the ancestral states in each character. You will find it
   useful to understand the difference between the Camin-Sokal parsimony
   criterion with unknown ancestral state and the Wagner parsimony
   criterion.

   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 invented by Kishino and Hasegawa (1989), and uses the mean
   and variance of step differences between trees, taken across
   characters. 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 highest one, the variance of that quantity as determined by the
   step differences at individual characters, 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 binary
   characters are evolving independently, which is unlikely to be true for
   many suites of morphological characters.

   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.

   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: mix.fmix


Mixed parsimony algorithm, version 3.69

Wagner parsimony method




     4 trees in all found




           +--Epsilon
     +-----4
     !     +--Gamma
  +--2
  !  !     +--Delta
--1  +-----3
  !        +--Beta
  !
  +-----------Alpha

  remember: this is an unrooted tree!


requires a total of      9.000





     +--------Gamma
     !
  +--2     +--Epsilon
  !  !  +--4
  !  +--3  +--Delta
--1     !
  !     +-----Beta
  !
  +-----------Alpha

  remember: this is an unrooted tree!


requires a total of      9.000





     +--------Epsilon
  +--4
  !  !  +-----Gamma
  !  +--2
--1     !  +--Delta
  !     +--3
  !        +--Beta
  !
  +-----------Alpha

  remember: this is an unrooted tree!


requires a total of      9.000





     +--------Gamma
  +--2
  !  !  +-----Epsilon
  !  +--4
--1     !  +--Delta
  !     +--3
  !        +--Beta
  !
  +-----------Alpha

  remember: this is an unrooted tree!


requires a total of      9.000



  File: mix.treefile

(((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.2500];
((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.2500];
((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.2500];
((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.2500];

  Output files for usage example 2

  File: mix.fmix


Mixed parsimony algorithm, version 3.69

5 species, 6 characters

Wagner parsimony method


Name         Characters
----         ----------

Alpha        11011 0
Beta         11000 0
Gamma        10011 0
Delta        00100 1
Epsilon      00111 0


    Ancestral states:
             001?? 1


One most parsimonious tree found:




  +-----------Delta
--3
  !  +--------Epsilon
  +--4
     !  +-----Gamma
     +--2
        !  +--Beta
        +--1
           +--Alpha


requires a total of      8.000

best guesses of ancestral states:
       0 1 2 3 4 5 6 7 8 9
     *--------------------
    0!   0 0 1 ? ? 1



  File: mix.treefile

(Delta,(Epsilon,(Gamma,(Beta,Alpha))));

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
                    fmove        Interactive mixed method parsimony
                    fpars        Discrete character 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.

                    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.
