EMBOSS: PHYLIP

| ## EMBOSS: PHYLIP

# Original PHYLIP mix documentation.

This is the original PHYLIP documentation and includes information on the old menu driven program which is now replaced with the EMBOSS acd file.

                                                                       version 3.5c

                             MIX - Mixed method parsimony

    (c) Copyright  1986-1993  by  Joseph  Felsenstein  and  by  the  University  of
    Washington.  Written by Joseph Felsenstein.  Permission is granted to copy this
    document provided that no fee is charged for it and that this copyright  notice
    is not removed.

         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).

                                     INPUT FORMAT

         The input for MIX is the standard input for discrete characters  programs,
    described above in the documentation file for the discrete-characters programs.
    States "?", "P", and "B" are allowed.

         The options are selected using a menu:

    Mixed parsimony algorithm, version 3.5c

    Settings for this run:
      U                 Search for best tree?  Yes
      X                     Use Mixed method?  No
      P                     Parsimony method?  Wagner
      J     Randomize input order of species?  No. Use input order
      O                        Outgroup root?  No, use as outgroup species  1
      T              Use Threshold parsimony?  No, use ordinary parsimony
      A   Use ancestral states in input file?  No
      M           Analyze multiple data sets?  No
      0   Terminal type (IBM PC, VT52, ANSI)?  ANSI
      1    Print out the data at start of run  No
      2  Print indications of progress of run  Yes
      3                        Print out tree  Yes
      4     Print out steps in each character  No
      5     Print states at all nodes of tree  No
      6       Write out trees onto tree file?  Yes

    Are these settings correct? (type Y or the letter for one to change)

         The options U, J, O, T,  A,  and  M  are  the  usual  User  Tree,  Jumble,
    Outgroup, Ancestral States, and Multiple Data Sets options, described either in
    the  main  documentation  file  or  in   the   Discrete   Characters   Programs
    documentation  file.   The  user-defined trees supplied if you use the U option
    must be given as rooted trees with two-way splits (bifurcations).  The O option
    is  acted  upon  only  if  the final tree is unrooted and is not a user-defined
    tree.  One of the important uses of the the O option is to  root  the  tree  so
    that  if  there  are any characters in which the ancestral states have not been
    specified, the program will print out a table showing  which  ancestral  states
    require the fewest steps.  Note that when any of the characters has Camin-Sokal
    parsimony assumed for it, the tree is rooted and the  O  option  will  have  no
    effect.

         The option P toggles between the Camin-Sokal parsimony criterion  and  the
    default  Wagner  parsimony criterion.  Option X invokes mixed-method parsimony.
    If the A option is invoked, the ancestor is not to be counted  as  one  of  the
    species.

         In the input file the W (Weights) option is available, as  usual.   The  A
    (Ancestral  states)  and  X  (Mixed  methods)  also  require  the options to be
    declared on the first line of the  input  file  and  other  information  to  be
    present  in the input file.  The Ancestral States option also requires that you
    choose the A option in the input menu.  Note that the X  option  requires  that
    the  option M (Mixture) be declared and the mixture information provided in the
    input file.  This is admittedly confusing.   The  F  (Factors)  option  is  not
    available  in  this  program,  as it would have no effect on the result even if
    that information were provided in the input file.

                                     OUTPUT FORMAT

         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 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   binary   characters   are   evolving
    independently,  which  is  unlikely to be true for many suites of morphological
    characters.

         At the beginning of the program are a series of constants,  which  can  be
    changed  to help adapt the program to different computer systems.  The constant
    "nmlngth" is the length of the species names.  "maxtrees" is the maximum number
    of  trees  which  the  program will store for output.  "maxuser" is the maximum
    number of user trees which can be input to the program.  You may want to change
    these constants to reduce memory requirements.

         The program is descended from earlier programs SOKAL and WAGNER which have
    since been removed from the PHYLIP package, since MIX has all their capabilites
    and more.

    -------------------------------TEST DATA SET----------------------------

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

    ---------- TEST SET OUTPUT (with all numerical options on) -------------

    Mixed parsimony algorithm, version 3.5c

    Wagner parsimony method

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

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

         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

     steps in each character:
             0   1   2   3   4   5   6   7   8   9
         *-----------------------------------------
        0!       2   2   2   1   1   1

    From    To     Any Steps?    State at upper node
                                 ( . means same as in the node below it on tree)

              1                1?011 0
      1       2         no     .?... .
      2       4        maybe   .0... .
      4    Epsilon      yes    0.1.. .
      4    Gamma        no     ..... .
      2       3         yes    .?.00 .
      3    Delta        yes    001.. 1
      3    Beta        maybe   .1... .
      1    Alpha       maybe   .1... .

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

      remember: this is an unrooted tree!

    requires a total of      9.000

     steps in each character:
             0   1   2   3   4   5   6   7   8   9
         *-----------------------------------------
        0!       1   2   1   2   2   1

    From    To     Any Steps?    State at upper node
                                 ( . means same as in the node below it on tree)

              1                1?011 0
      1       2         no     .?... .
      2    Gamma       maybe   .0... .
      2       3        maybe   .?.?? .
      3       4         yes    001?? .
      4    Epsilon     maybe   ...11 .
      4    Delta        yes    ...00 1
      3    Beta        maybe   .1.00 .
      1    Alpha       maybe   .1... .

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

      remember: this is an unrooted tree!

    requires a total of      9.000

     steps in each character:
             0   1   2   3   4   5   6   7   8   9
         *-----------------------------------------
        0!       2   2   2   1   1   1

    From    To     Any Steps?    State at upper node
                                 ( . means same as in the node below it on tree)

              1                1?011 0
      1       4        maybe   .0... .
      4    Epsilon      yes    0.1.. .
      4       2         no     ..... .
      2    Gamma        no     ..... .
      2       3         yes    ...00 .
      3    Delta        yes    0.1.. 1
      3    Beta         yes    .1... .
      1    Alpha       maybe   .1... .

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

      remember: this is an unrooted tree!

    requires a total of      9.000

     steps in each character:
             0   1   2   3   4   5   6   7   8   9
         *-----------------------------------------
        0!       2   2   2   1   1   1

    From    To     Any Steps?    State at upper node
                                 ( . means same as in the node below it on tree)

              1                1?011 0
      1       2        maybe   .0... .
      2    Gamma        no     ..... .
      2       4        maybe   ?.?.. .
      4    Epsilon     maybe   0.1.. .
      4       3         yes    ?.?00 .
      3    Delta        yes    0.1.. 1
      3    Beta         yes    110.. .
      1    Alpha       maybe   .1... .