version 3.4 FACTOR - Program to factor multistate characters.(c) Copyright 1986-1991 by Christopher A. Meacham. Permission is granted tocopy this document provided that no fee is charged for it and that thiscopyright notice is not removed. Programmed by C. Meacham, Botany, Univ. of Georgia, Athens, Georgia (current address: University Herbarium, University of California, Berkeley, California 94720) additional code 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, inturn, can be used as input to any of the other discrete character programs inthis package. Besides this primary function, FACTOR also provides an easy wayof deleting characters from a data set. The input format for FACTOR is verysimilar to the input format for the other discrete character programs exceptfor the addition of character-state tree descriptions. Note that this program has no way of converting an unordered multistatecharacter into binary characters. This is a weakness of the discretecharacters programs in this package. For the time being, the best I cansuggest is to code them as A, C, G, and T and use the DNA parsimony andcompatibility programs. That is not a very good alternative, admittedly. The first line of the input file should contain the number of species andthe number of multistate characters. This first line is followed by the linesdescribing the character-state trees, one description per line. The speciesinformation constitutes the last part of the file. Any number of lines may beused for a single species. FIRST LINE The first line is free format with the number of species first, separatedby at least one blank (space) from the number of multistate characters, whichin turn is separated by at least one blank from the options, if present. OPTIONSThe options are selected from a menu that looks like this:Factor -- multistate to binary recoding program, version 3.4Settings 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)? IBM PCAre these settings correct? (type Y or the letter for one to change) A Choosing the A (Ancestors) options toggles on and off the setting thatcauses 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, DOLMOVE, BOOT, and DOLBOOT use this information. CHARACTER-STATE TREE DESCRIPTIONS The character-state trees are described in free format. The characternumber of the multistate character is given first followed by the descriptionof the tree itself. Each description must be completed on a single line. Eachcharacter that is to be factored must have a description, and the charactersmust be described in the order that they occur in the input, that is, innumerical order. The tree is described by listing the pairs of character states that areadjacent to each other in the character-state tree. The two character statesin each adjacent pair are separated by a colon (':'). If character fifteen hasthis character state tree for possible states A ---- B ---- C ! ! ! Dthen the character-state tree description would be 15 A:B B:C D:BNote that either symbol may appear first. The ancestral state is identified,if desired, by putting it "adjacent" to a period. If we wanted to rootcharacter fifteen at state C: A <--- B <--- C ! ! V Dwe could write 15 B:D A:B C:B .:CBoth the order in which the pairs are listed and the order of the symbols ineach 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 characterthat signals the connection between two states (in the distribution copy thisis set to ':'), '.', and, of course, a blank. Blanks are ignored completely inthe tree description so that even B:DA:BC:B.:C or B : DA : BC : B. : C wouldbe equivalent to the above example. However, at least one blank must separatethe 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 numberis given on the line, but no character-state tree is provided, then the symbolfor the character in the input will be copied directly to the output withoutchange. 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 areto appear in the output. TERMINATING THE LIST OF TREE DESCRIPTIONS The last character-state tree description should be followed by a linecontaining the number '999'. This terminates processing of the trees andindicates the beginning of the species information. SPECIES INFORMATION The format for the species information is basically identical to the otherdiscrete character programs. The first ten character positions are allotted tothe species name (this value may be changed by