version 3.5c
SEQBOOT -- Bootstrap, Jackknife, or Permutation Resampling of
Molecular Sequence, Restriction Site, Gene Frequency or Character Data
(c) Copyright 1991-1993 by the University of Washington and by Joseph
Felsenstein. 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.
SEQBOOT is a general boostrapping tool. It is intended to allow you to
generate multiple data sets that are resampled versions of the input data set.
Since almost all programs in the package can analyze these multiple data sets,
this allows almost anything in this package to be bootstrapped, jackknifed, or
permuted. SEQBOOT can handle molecular sequences, binary characters,
restriction sites, or gene frequencies.
To carry out a bootstrap (or jackknife, or permutation test) with some
method in the package, you may need to use three programs. First, you need to
run SEQBOOT to take the original data set and produce a large number (say 100)
of bootstrapped data sets. Then you need to find the phylogeny estimate for
each of these, using the particular method of interest. For example, if you
were using DNAPARS you would first run SEQBOOT and make a file with 100
bootstrapped data sets. Then you would give this file the proper name to have
it be the input file for DNAPARS. Running DNAPARS with the M (Multiple Data
Sets) menu choice and informaing it to expect 100 data sets, you would generate
a big output file as well as a treefile with the trees from the 100 data sets.
This treefile could be renamed so that it would serve as the input for
CONSENSE. When CONSENSE is run the majority rule consensus tree will result,
showing the outcome of the analysis.
This may sound tedious, but the run of CONSENSE is fast, and that of
SEQBOOT is fairly fast, so that it will not actually take any longer than a run
of a single bootstrap program with the same original data and the same number
of replicates. It is not very hard and allows bootstrapping on many of the
methods in this package. The same steps are necessary with all of them. Doing
things this way some of the intermediate files (the tree file from the DNAPARS
run, for example) can be used to summarize the results of the bootstrap in
other ways than the majority rule consensus method does.
If you are using the Distance Matrix programs, you will have to add one
extra step to this, calculating distance matrices from each of the replicate
data sets, using DNADIST or GENDIST. So (for example) you would run SEQBOOT,
then run DNADIST using the output of SEQBOOT as its input, then run (say)
NEIGHBOR using the output of DNADIST as its input, and then run CONSENSE using
the tree file from NEIGHBOR as its input.
The resampling methods available are three:
1. The bootstrap. Bootstrapping was invented by Bradley Efron in 1979, and
its use in phylogeny estimation was introduced by me (Felsenstein, 1985b). It
involves creating a new data set by sampling N characters randomly with
replacement, so that the resulting data set has the same size as the original,
but some characters have been left out and others are duplicated. The random
variation of the results from analyzing these bootstrapped data sets can be
shown statistically to be typical of the variation that you would get from
collecting new data sets. The method assumes that the characters evolve
independently, an assumption that may not be realistic for many kinds of data.
2. Delete-half-jackknifing. This alternative to the bootstrap involves
sampling a random half of the characters, and including them in the data but
dropping the others. The resulting data sets are half the size of the
original, and no characters are duplicated. The random variation from doing
this should be very similar to that obtained from the bootstrap. The method is
advocated by Wu (1986).
3. Permuting species within characters. This method of resampling (well, OK,
it may not be best to call it resampling) was introduced by Archie (1989) and
Faith (1990; see also Faith and Cranston, 1991). It involves permuting the
columns of the data matrix separately. This produces data matrices that have
the same number and kinds of characters but no taxonomic structure. It is used
for different purposes than the bootstrap, as it tests not the variation around
an estimated tree but the hypothesis that there is no taxonomic structure in
the data: if a statistic such as number of steps is significantly smaller in
the actual data than it is in replicates that are permuted, then we can argue
that there is some taxonomic structure in the data (though perhaps it might be
just a pair of sibling species).
The data input file is of standard form for molecular sequences (either in
interleaved or sequential form), restriction sites, gene frequencies, or binary
morphological characters. The only options that can be present in the input
file are W (Weights) and F (Factors), the latter only in the case of binary
(0,1) characters. The Weights can only be 0 or 1, and act to select the
characters (or sites) that will be used in the resampling, the others being
ignored and always omitted from the output data sets. The Factors option
allows us to specify that groups of binary characters represent one multistate
character. When sampling is done they will be sampled or omitted together, and
when permutations of species are done they will all have the same permutation,
as would happen if they really were just one column in the data matrix. For
futher description of the F (Factors) option see the Discrete Characters
Programs documentation file.
When the program runs it first asks you for a random number seed. This
should be an integer greater than zero (and probably less than 32767) and which
is of the form 4n+1, that is, it leaves a remainder of 1 when divided by 4.
This can be judged by looking at the last two digits of the integer (for
instance 7651 is not of form 4n+1 as 51, when divided by 4, leaves the
remainder 3).
Then the program shows you a menu to allow you to choose options. The
menu looks like this:
Bootstrapped sequences algorithm, version 3.5c
Settings for this run:
D Sequence, Morph, Rest., Gene Freqs? Molecular sequences
J Bootstrap, Jackknife, or Permute? Bootstrap
R How many replicates? 100
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
Are these settings correct? (type Y or the letter for one to change)
The user selects options by typing D, J, R, I, 0, 1, or 2, and continues to do
so until all options are correctly set. Then the program can be run by typing
Y. The 0 (Terminal type) option is the usual one.
It is important to select the correct data type (the D selection). Each
time D is typed the program will change data type, proceeding successively
through Molecular Sequences, Discrete Morphological Characters, Restriction
Sites, and Gene Frequencies. Some of these will cause additional entries to
appear in the menu. If Molecular Sequences or Restriction Sites settintgs and
chosen the I (Interleaved) option appears in the menu (and as Molecular
Sequences are also the default, it appears in the first menu). It is the usual
I option discussed in the Molecular Sequences document file and in the main
documentation files for the package.
If the Restriction Sites option is chosen the menu option E appears, which
asks whether the input file contains a third number on the first line of the
file, for the number of restriction enzymes used to detect these sites. This
is necessary because data sets for RESTML need this third number, but other
programs do not, and SEQBOOT needs to know what to expect.
If the Gene Frequencies option is chosen an menu option A appears which
allows the user to specify that all alleles at each locus are in the input
file. The default setting is that one allele is absent at each locus.
The J option allows the user to select Bootstrapping, Delete-Half-
Jackknifing, or the Archie-Faith permutation of species within characters. It
changes successively among these three each time J is typed.
The R option allows the user to set the number of replicate data sets.
This defaults to 100. Most statisticians would be happiest with 1000 to 10,000
replicates in a bootstrap, but 100 gives a good rough picture. You will have
to decide this based on how long a running time you want.
Input File
The data files read by SEQBOOT are the standard ones for the various kinds
of data. For molecular sequences the sequences may be either interleaved or
sequential, and similarly for restriction sites. Restriction sites data may
either have or not have the third argument, the number of restriction enzymes
used. Discrete morphological characters are always assumed to be in sequential
format. Gene frequencies data start with the number of species and the number
of loci, and then follow that by a line with the number of alleles at each
locus. The data for each locus may either have one entry for each allele, or
omit one allele at each locus. The details of the formats are given in the
main documentation file, and in the documentation files for the groups of
programs.
There are relatively few options specified in the input file. The Weights
option is allowed (in all cases). So is the Factors option for Discrete
Morphological Characters. Other options are not allowed. This is a serious
limitation of the program, as users may want to pass other options on to the
output data files, for use in the programs. In future versions I hope to
gradually add some of the options, particulary the A (Ancestors) option for
discrete morphological characters. For the moment if you want to put any such
options in you would have to edit them into the output by hand, which will be
difficult since the identities of the characters in different columns of the
output file will vary as a result of the bootstrapping or jackknifing process.
Output
The output file will contain the data sets generated by the resampling
process. Note that, when Gene Frequencies data is used or when Discrete
Morphological characters with the Factors option are used, the number of
characters in each data set may vary. It may also vary if there are an odd
number of characters or sites and the Delete-Half-Jackknife resampling method
is used, for then there will be a 50% chance of choosing (n+1)/2 characters and
a 50% chance of choosing (n-1)/2 characters.
The numerical options 1 and 2 in the menu also affect the output file. If
1 is chosen (it is off by default) the program will print the original input
data set on the output file before the resampled data sets. I cannot actually
see why anyone would want to do this. Option 2 toggles the feature (on by
default) that prints out up to 20 times during the resampling process
notification that the program has completed a certain number of data sets.
Thus if 100 resampled data sets are being produced, every 5 data sets a line is
printed saying which data set has just been completed. This option should be
turned off if the program is running in background and silence is desirable.
At the end of execution the program will always (whatever the setting of option
2) print a couple of lines saying that output has been written to the output
file.
Size and Speed
The program runs moderately quickly, though more slowly when the
Permutation resampling method is used than with the others. Constants
available are "nmlngth", the length of a species name, and the boolean
constants "ibmpc0:, "ansi0", and "vt520" if that terminal type (IBM PC, VT52,
or ANSI) is to be the default when the program first runs and false otherwise.
Future
I hope in the future to include code to pass on the Ancestors and
Categories options from the input file to the output file, a serious omission
in the current version. Already, this program has made the bootstrap programs
DNABOOT, BOOT, and DOLBOOT obsolete, and they have been dropped from the
package. SEQBOOT's use results in a result identical to those programs if
DNAPARS, MIX and DOLLOP are run on the output from SEQBOOT, except for getting
a different sequence of random numbers.
------------------ TEST DATA SET --------------------------
5 6
Alpha AACAAC
Beta AACCCC
Gamma ACCAAC
Delta CCACCA
Epsilon CCAAAC
--- CONTENTS OF OUTPUT FILE IF REPLICATES ARE SET TO 10 AND SEED TO 4331 ---
5 6
Alpha ACCCAC
Beta ACCCCC
Gamma CCCCAC
Delta CAAACA
Epsilon CAAAAC
5 6
Alpha AAAACC
Beta AACCCC
Gamma ACAACC
Delta CCCCAA
Epsilon CCAACC
5 6
Alpha AAAAAC
Beta AACCCC
Gamma CCAAAC
Delta CCCCCA
Epsilon CCAAAC
5 6
Alpha AAAAAA
Beta AACCCC
Gamma ACAAAA
Delta CCCCCC
Epsilon CCAAAA
5 6
Alpha ACCCAA
Beta ACCCCC
Gamma CCCCAA
Delta CAAACC
Epsilon CAAAAA
5 6
Alpha AAACCC
Beta AAACCC
Gamma AACCCC
Delta CCCAAA
Epsilon CCCACC
5 6
Alpha AACAAC
Beta AACCCC
Gamma ACCAAC
Delta CCACCA
Epsilon CCAAAC
5 6
Alpha ACCCAA
Beta ACCCCC
Gamma ACCCAA
Delta CAAACC
Epsilon CAAAAA
5 6
Alpha AACACC
Beta AACCCC
Gamma ACCACC
Delta CCACAA
Epsilon CCAACC
5 6
Alpha AAAACA
Beta AAAACC
Gamma AAAACA
Delta CCCCAC
Epsilon CCCCAA