Change from an occupied site to a deletion is counted as one change. Reversion from a deletion to an occupied site is allowed and is also counted as one change. Note that this in effect assumes that a deletion N bases long is N separate events.
The input data is standard. The first line of the input file contains the number of species and the number of sites. If the Weights option is being used, there must also be a W in this first line to signal its presence. There are only two options requiring information to be present in the input file, W (Weights) and U (User tree). All options other than W are invoked using the menu.
Next come the species data. Each sequence starts on a new line, has a ten-character species name that must be blank-filled to be of that length, followed immediately by the species data in the one-letter code. The sequences must either be in the "interleaved" or "sequential" formats described in the Molecular Sequence Programs document. The I option selects between them. The sequences can have internal blanks in the sequence but there must be no extra blanks at the end of the terminated line. Note that a blank is not a valid symbol for a deletion.
The options are selected using an interactive menu. The menu looks like this:
DNA parsimony algorithm, version 3.5c Setting for this run: U Search for best tree? Yes J Randomize input order of sequences? No. Use input order O Outgroup root? No, use as outgroup species 1 T Use Threshold parsimony? No, use ordinary parsimony M Analyze multiple data sets? No I Input sequences interleaved? Yes 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 site No 5 Print sequences 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 user either types "Y" (followed, of course, by a carriage-return) if the settings shown are to be accepted, or the letter or digit corresponding to an option that is to be changed.
The options U, J, O, T, M, and 0 are the usual ones. They are described in the main documentation file of this package. Option I is the same as in other molecular sequence programs and is described in the molecular sequence programs documentation.
The O (outgroup) option will have no effect if the U (user-defined tree) option is in effect. The user trees (U option) should be rooted bifurcating trees. 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!
Output is standard: if option 1 is toggled on, the data is printed out, with the convention that "." means "the same as in the first species". Then comes a list of equally parsimonious trees, and (if option 2 is toggled on) a table of the number of changes of state required in each character. If option 5 is toggled on, 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 "?" or one of the IUB ambiguity symbols, there will be multiple equally- parsimonious assignments of states; the user must work these out for themselves by hand. A "?" in the reconstructed states means that in addition to one or more bases, a deletion may or may not be present. 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 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 due to Kishino and Hasegawa (1989), and uses the mean and variance of step differences between trees, taken across sites. 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 best 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.
The program is a straightforward relative of MIX and runs reasonably quickly, especially with many sites and few species.
TEST DATA SET
CONTENTS OF OUTPUT FILE (if all numerical options are on)
DNA parsimony algorithm, version 3.5c
Alpha AACGUGGCCA AAU
Beta ..G..C.... ..C
Gamma C.UU.C.U.. C.A
Delta GGUA.UU.GG CC.
Epsilon GGGA.CU.GG CCC
One most parsimonious tree found:
remember: this is an unrooted tree!
requires a total of 19.000
steps in each site:
0 1 2 3 4 5 6 7 8 9
0! 2 1 3 2 0 2 1 1 1
10! 1 1 1 3
From To Any Steps? State at upper node
( . means same as in the node below it on tree)
1 AABGTSGCCA AAY
1 2 maybe .....C.... ...
2 3 yes V.KD...... C..
3 4 yes GG.A..T.GG .C.
4 Epsilon maybe ..G....... ..C
4 Delta yes ..T..T.... ..T
3 Gamma yes C.TT...T.. ..A
2 Beta maybe ..G....... ..C
1 Alpha maybe ..C..G.... ..T
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