version 3.5c


                   MOVE - Interactive 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.

     MOVE is an interactive parsimony program, inspired by Wayne  Maddison  and
David  Maddison's  marvellous  program  MacClade,  which  is  written for Apple
Macintosh computers.  MOVE reads in a data set which is prepared in almost  the
same  format  as one for the mixed method parsimony program MIX.  It allows the
user to choose an initial tree, and displays this tree on the screen.  The user
can  look  at  different characters and the way their states are distributed on
that tree, given the most parsimonious reconstruction of state changes for that
particular tree.  The user then can specify how the tree is to be rearraranged,
rerooted or written out to a file.  By looking at different  rearrangements  of
the  tree  the user can manually search for the most parsimonious tree, and can
get a feel for how different characters are affected by  changes  in  the  tree
topology.

     This program is compatible with fewer  computer  systems  than  the  other
programs  in PHYLIP.  It can be adapted to PCDOS systems or to any system whose
screen or terminals emulate DEC VT52 or VT100 terminals (such as, for  example,
Zenith  Z19,  Z29,  and Z49 terminals, Telnet programs for logging in to remote
computers over a TCP/IP network, VT100-compatible windows in  the  X  windowing
system,  and  any  terminal compatible with ANSI standard terminals).   For any
other screen types, there is a generic option which does not make use of screen
graphics  characters  to  display  the  character  states.   This  will be less
effective, as the states will be less easy to see when displayed.

     The input data file is set up almost identically to  the  data  files  for
MIX.   The sole exception is that the user trees are not contained in the input
file, but in the tree file, which is used both for input of the  starting  tree
(if  desired)  and for output of the final tree.  Note that this means that the
user tree supplied on input will possibly be overwritten.  The W  (Weights),  A
(Ancestors),  M  (Mixed methods) and F (Factors) are possible options specified
in the input file (some must also be chosen in the menu).

     The user interaction starts with the program presenting a menu.  The  menu
looks like this:


Interactive mixed parsimony algorithm, version 3.4

Settings for this run:
  X                        Use Mixed method?  No
  P                        Parsimony method?  Wagner
  A      Use ancestral states in input file?  No
  O                           Outgroup root?  No, use as outgroup species   1
  T                 Use Threshold parsimony?  No, use ordinary parsimony
  U Initial tree (arbitrary, user, specify)?  Arbitrary
  0      Graphics type (IBM PC, VT52, ANSI)?  ANSI
  L               Number of lines on screen?  24

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

The O (Outgroup), T (Threshold), and 0 (Graphics type) options  are  the  usual


ones and are described in the main documentation file.  The L option allows the
program to take advanatage of  larger  screens  if  available.   The  X  (Mixed
method)  option  is  described in the Discrete Characters Programs docmentation
file.   It  requires  information  on  the  parsimony  methods  for   different
characters  to  be  in  the input file.  The U (initial tree) option allows the
user to choose whether the initial  tree  is  to  be  arbitrary,  interactively
specified  by  the user, or read from a tree file.  Typing U causes the program
to change among the three possibilities in turn.  I would recommend that for  a
first  run,  you  allow the tree to be set up arbitrarily (the default), as the
"specify" choice is difficult to use and the "user tree" choice  requires  that
you  have available a tree file with the tree topology of the initial tree.  If
you wish to  set  up  some  particular  tree  you  can  also  do  that  by  the
rearrangement  commands  specified  below.   The  T (threshold) option allows a
continuum of methods between parsimony and compatibility.  Thresholds less than
or  equal  to  1.0  do  not  have any meaning and should not be used: they will
result in a tree dependent only on the input order of species and not at all on
the data!

     After the initial menu is displayed and the choices are made, the  program
then sets up an initial tree and displays it.  Below it will be a one-line menu
of possible commands, which looks like this:

NEXT? (Options: R # + - S . T U W O F C H ? X Q) (H or ? for Help)

If you type H or ? you will get a single screen showing a description  of  each
of   these   commands  in  a  few  words.   Here  are  slightly  more  detailed
descriptions:

R    ("Rearrange").  This command asks for the number of a node which is to  be
    removed from the tree.  It and everything to the right of it on the tree is
    to be removed (by breaking the branch immediately below it).   The  command
    also  asks  for  the  number  of  a  node  below  which that group is to be
    inserted.  If an impossible number is given, the program refuses  to  carry
    out  the  rearrangement and asks for a new command.  The rearranged tree is
    displayed: it will  often  have  a  different  number  of  steps  than  the
    original.   If  you wish to undo a rearrangement, use the Undo command, for
    which see below.

#    This command, and the +, - and S commands described below, determine which
    character  has  its  states  displayed  on  the branches of the trees.  The
    initial tree displayed by the program does not show states of sites.   When
    #  is  typed,  the  program  does not ask the user which character is to be
    shown but automatically shows the states of the next binary character  that
    is not compatible with the tree (the next character that does not perfectly
    fit the current tree).  The search for this  character  "wraps  around"  so
    that  if  it  reaches  the  last  character without finding one that is not
    compatible with the tree, the search continues at the first  character;  if
    no  incompatible  character is found the current character is shown, and if
    no current character is shown then  the  first  character  is  shown.   The
    display  takes the form of different symbols or textures on the branches of
    the tree.  The state of each branch is actually the state of the node above
    it.   A key of the symbols or shadings used for states 0, 1 and ? are shown
    next to the tree.  State ? means that either state 0 or state 1 could exist
    at  that  point  on  the  tree,  and that the user may want to consider the
    different possibilities, which are usually apparent by inspection.

+    This command is the same as # except that it goes forward  one  character,
    showing  the states of the next character.  If no character has been shown,
    using + will cause  the  first  character  to  be  shown.   Once  the  last
    character has been reached, using + again will show the first character.



-    This command is the same as + except that it goes backwards,  showing  the
    states  of the previous character.  If no character has been shown, using -
    will cause the last character to be shown.  Once  character  number  1  has
    been reached, using - again will show the last character.

S    ("Show").  This command is the same as + and - except that it  causes  the
    program  to  ask  you for the number of a character.  That character is the
    one whose states will be displayed.  If you give the character number as 0,
    the program will go back to not showing the states of the characters.

 .    This command simply causes the current tree to be redisplayed.  It is  of
    use when the tree has partly disappeared off of the top of the screen owing
    to too many responses to commands being printed out at the  bottom  of  the
    screen.

T    ("Try rearrangements").  This command asks for the name of  a  node.   The
    part  of  the  tree  at  and above that node is removed from the tree.  The
    program tries to re-insert it in each possible location on the  tree  (this
    may  take  some time, and the program reminds you to wait).  Then it prints
    out a summary.  For each possible  location  the  program  prints  out  the
    number of the node to the right of the place of insertion and the number of
    steps required in each case.  These are divided into those that are better,
    tied,  or  worse  than the current tree.  Once this summary is printed out,
    the group that was removed is inserted into its original position.   It  is
    up  to  you to use the R command to actually carry out any the arrangements
    that have been tried.

U     ("Undo").   This  command  reverses  the  effect  of  the   most   recent
    rearrangement, outgroup re-rooting, or flipping of branches.  It returns to
    the previous tree topology.  It will be of great use when  rearranging  the
    tree  and  when  a  rearrangement proves worse than the preceding one -- it
    permits you to abandon the new one and return to the previous  one  without
    remembering its topology in detail.

W    ("Write").  This command writes out the current tree onto  a  tree  output
    file.  If the file already has been written to by this run of MOVE, it will
    ask you whether you want to replace the contents of the file, add the  tree
    to the end of the file, or not write out the tree to the file.  The tree is
    written in the standard  format  used  by  PHYLIP  (a  subset  of  the  New
    Hampshire  standard).   It  is  in  the proper format to serve as the User-
    Defined Tree for setting up the initial tree in a  subsequent  run  of  the
    program.   Note  that  if  you provided the initial tree topology in a tree
    file and replace its contents, that initial tree will be lost.

O    ("Outgroup").  This asks for the number of a  node  which  is  to  be  the
    outgroup.   The  tree  will  be  redisplayed  with  that  node  as the left
    descendant of the bottom fork.  Under some options (for example the  Camin-
    Sokal  parsimony method or the Ancestor state options), the number of steps
    required on the tree may change on re-rooting.  Note that it is possible to
    use this to make a multi-species group the outgroup (i.e., you can give the
    number of an interior node of the tree as the  outgroup,  and  the  program
    will re-root the tree properly with that on the left of the bottom fork).

F    ("Flip").  This asks for a node number and then flips the two branches  at
    that  node,  so  that  the  left-right  order  of  branches at that node is
    changed.  This does not actually change the tree topology (or the number of
    steps on that tree) but it does change the appearance of the tree.

C    ("Clade").  When the data consist of more than 12 species  (or  more  than
    half  the  number  of  lines  on  the  screen if this is not 24), it may be
    difficult to display the tree on one screen.  In that case the tree will be


    squeezed  down  to  one line per species.  This is too small to see all the
    interior states of the tree.  The C command instructs the program to  print
    out  only  that  part  of the tree (the "clade") from a certain node on up.
    The program will prompt you for the number of  this  node.   Remember  that
    thereafter you are not looking at the whole tree.  To go back to looking at
    the whole tree give the C command again and enter "0" for the  node  number
    when asked.  Most users will not want to use this option unless forced to.

H    ("Help").  Prints a one-screen summary of what  the  commands  do,  a  few
    words for each command.

?    ("?").  A synonym for H.  Same as Help command.

X    ("Exit").  Exit from program.  If the current tree has not yet been  saved
    into a file, the program will ask you whether it should be saved.

Q    ("Quit").  A synonym for X.  Same as the eXit command.

     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 information to be  present  in
the  input  file.   If the Ancestral States option is invoked the A option must
also be chosen from the 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  available  in  this
program.  It is used to inform the program which groups of characters are to be
counted together in computing the number  of  characters  compatible  with  the
tree.   Thus  if three binary characters are all factors of the same multistate
character, the multistate character will be counted as compatible with the tree
only if all three factors are compatible with it.


          ADAPTING THE PROGRAM TO YOUR COMPUTER AND TO YOUR TERMINAL

     As we have seen, the initial menu of the  program  allows  you  to  choose
among  four  screen  types  (PCDOS, Ansi, VT52 and none).  If you want to avoid
having to make this choice every time, you can change some of the constants  at
the  beginning  of  the program to have it initialize itself in the proper way,
and recompile it.  Among the constants at the beginning of the program you will
find  three  that determine which kind of screen graphics the program will use.
These constants are "ibmpc0",  "vt520",  and  "ansi0".    In  the  distribution
version  of  the  programs,  "ansi0" is set to true and the others to false, so
that the version will work with ANSI compatible terminals.

     On the other hand if you have a terminal compatible with DEC's  VT52,  but
not with the ANSI terminal, you should change the constant "ansi0" to false and
"vt520" to true.   If you have instead a terminal which is compatible with  IBM
PC  graphics,  you  should  set the constant "ibmpc0" to true and the others to
false.   If your terminal is compatible with none of these, you  will  have  to
set the constants all false, in which case special graphics characters will not
be used to indicate character states, but only "*" for 1, "=" for  0,  and  "."
for ? states.  This is less easy to look at.

     The program should work successfully on DEC VAX systems under  either  the
VMS or the Unix operating systems without any other changes.

                      MORE ABOUT THE PARSIMONY CRITERION

     MOVE uses as its numerical criterion 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).


                                   CONSTANTS

     At the beginning of the program are a series of constants,  which  can  be
changed  to help adapt the program to different computer systems.  "nmlngth" is
the length of the species names.  "screenlines" specifies the number  of  lines
per  screen,  which you will normally want to leave at its default value of 24.
I have already described the  constants  "ibmpc0",  "vt520",  and  "ansi0"  for
specifying the terminal type.

     Below is a test data set, but we  cannot  show  the  output  it  generates
because of the interactive nature of the program.

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

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