FACTOR - Program to factor multistate characters.
(c) Copyright 1986-1993 by Christopher A. Meacham. Permission is granted to
copy this document provided that no fee is charged for it and that this
copyright notice is not removed.
Programmed by C. Meacham, Botany, Univ. of Georgia, Athens, Georgia
(current address: University of California, Berkeley, California 94720)
additional code and documentation by Joe Felsenstein
This program factors a data set that contains multistate characters,
creating a data set consisting entirely of binary (0,1) characters that, in
turn, can be used as input to any of the other discrete character programs in
this package. Besides this primary function, FACTOR also provides an easy way
of deleting characters from a data set. The input format for FACTOR is very
similar to the input format for the other discrete character programs except
for the addition of character-state tree descriptions.
Note that this program has no way of converting an unordered multistate
character into binary characters. This is a weakness of the discrete
characters programs in this package. For the time being, the best I can
suggest is to code them as A, C, G, and T and use the DNA parsimony and
compatibility programs. That is not a very good alternative, admittedly.
The first line of the input file should contain the number of species and
the number of multistate characters. This first line is followed by the lines
describing the character-state trees, one description per line. The species
information constitutes the last part of the file. Any number of lines may be
used for a single species.
The first line is free format with the number of species first, separated
by at least one blank (space) from the number of multistate characters, which
in turn is separated by at least one blank from the options, if present.
The options are selected from a menu that looks like this:
Factor -- multistate to binary recoding program, version 3.5c
Settings for this run:
A put ancestral states in output file? No
F put factors information in output file? No
0 Terminal type (IBM PC, VT52, ANSI)? ANSI
Are these settings correct? (type Y or the letter for one to change)
A Choosing the A (Ancestors) options toggles on and off the setting that
causes a line to be written in the output that describes the states of the
ancestor as indicated by the character-state tree descriptions (see
below). If the ancestral state is not specified by a particular
character-state tree, a '?' signifying an unknown character state will be
written. The multistate characters are factored in such a way that the
ancestral state in the factored data set will always be '0'. The ancestor
line does not get counted as a species.
F Choosing the F (Factors) option toggles on and off a setting that will
cause a 'FACTORS' line to be written in the output. This line will
indicate to other programs which factors came from the same multistate
character. Of the programs currently in the package only SEQBOOT, MOVE,
and DOLMOVE use this information.
CHARACTER-STATE TREE DESCRIPTIONS
The character-state trees are described in free format. The character
number of the multistate character is given first followed by the description
of the tree itself. Each description must be completed on a single line. Each
character that is to be factored must have a description, and the characters
must be described in the order that they occur in the input, that is, in
The tree is described by listing the pairs of character states that are
adjacent to each other in the character-state tree. The two character states
in each adjacent pair are separated by a colon (':'). If character fifteen has
this character state tree for possible states
A ---- B ---- C
then the character-state tree description would be
15 A:B B:C D:B
Note that either symbol may appear first. The ancestral state is identified,
if desired, by putting it "adjacent" to a period. If we wanted to root
character fifteen at state C:
A <--- B <--- C
we could write
15 B:D A:B C:B .:C
Both the order in which the pairs are listed and the order of the symbols in
each pair are arbitrary. However, each pair may only appear once in the list.
Any symbols may be used for a character state in the input except the character
that signals the connection between two states (in the distribution copy this
is set to ':'), '.', and, of course, a blank. Blanks are ignored completely in
the tree description so that even B:DA:BC:B.:C or B : DA : BC : B. : C would
be equivalent to the above example. However, at least one blank must separate
the character number from the tree description.
DELETING CHARACTERS FROM A DATA SET
If no description line appears in the input for a particular character,
then that character will be omitted from the output. If the character number
is given on the line, but no character-state tree is provided, then the symbol
for the character in the input will be copied directly to the output without
change. This is useful for characters that are already coded '0' and '1'.
Characters can be deleted from a data set simply by listing only those that are
to appear in the output.
TERMINATING THE LIST OF TREE DESCRIPTIONS
The last character-state tree description should be followed by a line
containing the number '999'. This terminates processing of the trees and
indicates the beginning of the species information.
The format for the species information is basically identical to the other
discrete character programs. The first ten character positions are allotted to
the species name (this value may be changed by altering the value of the
constant nmlngth at the beginning of the program). The character states follow
and may be continued to as many lines as desired. There is no current method
for indicating polymorphisms. It is possible to either put blanks between
characters or not.
There is a method for indicating uncertainty about states. There is one
character value that stands for 'unknown'. If this appears in the input data
then '?' is written out in all the corresponding positions in the output file.
The character value that designates program, and can be changed by changing
that constant. It is set to
The first line of output will contain the number of species and the number
of binary characters in the factored data set followed by the letter 'A' if the
A option was specified in the input. If option F was specified, the next line
will begin 'FACTORS'. If option A was specified, the line describing the
ancestor will follow next. Finally, the factored characters will be written
for each species in the format required for input by the other discrete
programs in the package. The maximum length of the output lines is 80
characters, but this maximum length can be changed prior to compilation.
The output should be checked for error messages. Errors will occur in the
character-state tree descriptions if the format is incorrect (colons in the
wrong place, etc.), if more than one root is specified, if the tree contains
loops (and hence is not a tree), and if the tree is not connected, e.g.
A:B B:C D:E
A ---- B ---- C D ---- E
This "tree" is in two unconnected pieces. An error will also occur if a symbol
appears in the data set that is not in the tree description for that character.
Blanks at the end of lines when the species information is continued to a new
line will cause this kind of error.
CONSTANTS AVAILABLE TO BE CHANGED
At the beginning of the program a number of are available to be changed to
accomodate larger data sets. These are "nmlngth", "maxstates", "maxoutput",
"sizearray", "factchar" and "unkchar". The constant "nmlngth" is the length of
the species name. The allowed in the input. The CONSTant maxstates constant
"maxstates" gives the maximum number of states per character (set at 20 in the
distribution copy). The constant "maxoutput" gives the maximum width of a line
in the output file (80 in the distribution copy). The constant "sizearray"
must be less than the sum of squares of the numbers of states in the
characters. It is initially set to set to 2000, so that although 20 states are
allowed (at the initial setting of maxstates) per character, there cannot be 20
states in all of 100 characters.
Particularly important constants are "factchar" and "unkchar" which are
not numerical values but a character. Initially set to the colon ':',
"factchar" is the character that will be used to separate states in the input
of character state trees. It can be changed by changing this constant. (We
could have used a hyphen ('-') but didn't because that would make the minus-
sign ('-') unavailable as a character state in +/- characters). The constant
"unkchar" is the character value in the input data that indicates that the
state is unknown. It is set to '?' in the distribution copy. If your computer
is one that lacks the colon ':' in its character set or uses a nonstandard
character code such as EBCDIC, you will want to change the constant "factchar".
INPUT AND OUTPUT FILES
The input file for the program has the default file name "infile" and the
output file, the one that has the binary character state data, has the name
----SAMPLE INPUT----- -----Comments (not part of input file) -----
4 6 A 4 species; 6 characters; A option on
1 A:B B:C A ---- B ---- C
2 A:B B:. B ---> A
4 Character 3 deleted; 4 unchanged
5 0:1 1:2 .:0 0 ---> 1 ---> 2
6 .:# #:$ #:% # ---> $ ---> %
999 Signals end of trees
Alpha CAW00# Species information begins
---SAMPLE OUTPUT----- -----Comments (not part of input file) -----
5 8 A 5 species (incl. anc.); 8 factors
ANCESTOR ??0?0000 Chars. 1 and 2 come from old number 1
Alpha 11100000 Char. 3 comes from old number 2
Beta 10001001 Char. 4 is old number 4
Gamma 00011100 Chars. 5 and 6 come from old number 5
Epsilon 11101010 Chars. 7 and 8 come from old number 6