EMBOSS: frestboot

frestboot

Wiki

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Function

Bootstrapped restriction sites algorithm

Description

Reads in a data set, and produces multiple data sets from it by bootstrap resampling. Since most programs in the current version of the package allow processing of multiple data sets, this can be used together with the consensus tree program CONSENSE to do bootstrap (or delete-half-jackknife) analyses with most of the methods in this package. This program also allows the Archie/Faith technique of permutation of species within characters. It can also rewrite a data set to convert it from between the PHYLIP Interleaved and Sequential forms, and into a preliminary version of a new XML sequence alignment format which is under development

Algorithm

FRESTBOOT is a restriction site specific version of SEQBOOT.

SEQBOOT is a general bootstrapping and data set translation 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. It can also convert data sets between Sequential and Interleaved format, and into the NEXUS format or into a new XML sequence alignment format.

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 of bootstrapped or jackknifed data sets (somewhere between 100 and 1000 is usually adequate). 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 informing 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. This is not very hard and allows bootstrapping or jackknifing 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:

The bootstrap. Bootstrapping was invented by Bradley Efron in 1979, and its use in phylogeny estimation was introduced by me (Felsenstein, 1985b; see also Penny and Hendy, 1985). 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.
The partial bootstrap.. This is the bootstrap where fewer than the full number of characters are sampled. The user is asked for the fraction of characters to be sampled. It is primarily useful in carrying out Zharkikh and Li's (1995) Complete And Partial Bootstrap method, and Shimodaira's (2002) AU method, both of which correct the bias of bootstrap P values.
Block-bootstrapping. One pattern of departure from indeopendence of character evolution is correlation of evolution in adjacent characters. When this is thought to have occurred, we can correct for it by samopling, not individual characters, but blocks of adjacent characters. This is called a block bootstrap and was introduced by Künsch (1989). If the correlations are believed to extend over some number of characters, you choose a block size, B, that is larger than this, and choose N/B blocks of size B. In its implementation here the block bootstrap "wraps around" at the end of the characters (so that if a block starts in the last B-1 characters, it continues by wrapping around to the first character after it reaches the last character). Note also that if you have a DNA sequence data set of an exon of a coding region, you can ensure that equal numbers of first, second, and third coding positions are sampled by using the block bootstrap with B = 3.
Partial block-bootstrapping. Similar to partial bootstrapping except sampling blocks rather than single characters.
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). It was mentioned by me in my bootstrapping paper (Felsenstein, 1985b), and has been available for many years in this program as an option. Note that, for the present, block-jackknifing is not available, because I cannot figure out how to do it straightforwardly when the block size is not a divisor of the number of characters.
Delete-fraction jackknifing. Jackknifing is advocated by Farris et. al. (1996) but as deleting a fraction 1/e (1/2.71828). This retains too many characters and will lead to overconfidence in the resulting groups when there are conflicting characters. However it is made available here as an option, with the user asked to supply the fraction of characters that are to be retained.
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 the presence of aa pair of sibling species).
Permuting characters. This simply permutes the order of the characters, the same reordering being applied to all species. For many methods of tree inference this will make no difference to the outcome (unless one has rates of evolution correlated among adjacent sites). It is included as a possible step in carrying out a permutation test of homogeneity of characters (such as the Incongruence Length Difference test).
Permuting characters separately for each species. This is a method introduced by Steel, Lockhart, and Penny (1993) to permute data so as to destroy all phylogenetic structure, while keeping the base composition of each species the same as before. It shuffles the character order separately for each species.

Rewriting. This is not a resampling or permutation method: it simply rewrites the data set into a different format. That format can be the PHYLIP format. For molecular sequences and discrete morphological character it can also be the NEXUS format. For molecular sequences one other format is available, a new (and nonstandard) XML format of our own devising. When the PHYLIP format is chosen the data set is coverted between Interleaved and Sequential format. If it was read in as Interleaved sequences, it will be written out as Sequential format, and vice versa. The NEXUS format for molecular sequences is always written as interleaved sequences. The XML format is different from (though similar to) a number of other XML sequence alignment formats. An example will be found below. Here is a table to links to those other XML alignment formats:

Andrew Rambaut's BEAST XML format	http://evolve.zoo.ox.ac.uk/beast/introXML.html and http://evolve.zoo.ox.ac.uk/beast/referenindex.html	A format for alignments. There is also a format for phylogenies described there.
MSAML M	http://xml.coverpages.org/msaml-desc-dec.html	Defined by Paul Gordon of University of Calgary. See his big list of molecular biology XML projects.
BSML	http://www.bsml.org/resources/default.asp	Bioinformatic Sequence Markup Language includes a multiple sequence alignment XML format

Usage

Here is a sample session with frestboot

% frestboot -seed 3 Bootstrapped restriction sites algorithm Input file: restboot.dat Phylip seqboot_rest program output file [restboot.frestboot]: completed replicate number 10 completed replicate number 20 completed replicate number 30 completed replicate number 40 completed replicate number 50 completed replicate number 60 completed replicate number 70 completed replicate number 80 completed replicate number 90 completed replicate number 100 Output written to file "restboot.frestboot" Done.

Go to the input files for this example
Go to the output files for this example

Command line arguments

Bootstrapped restriction sites algorithm
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            discretestates File containing one or more sets of
                                  restriction data
  [-outfile]           outfile    [*.frestboot] Phylip seqboot_rest program
                                  output file

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -test               menu       [b] Choose test (Values: b (Bootstrap); j
                                  (Jackknife); c (Permute species for each
                                  character); o (Permute character order); s
                                  (Permute within species); r (Rewrite data))
*  -regular            toggle     [N] Altered sampling fraction
*  -fracsample         float      [100.0] Samples as percentage of sites
                                  (Number from 0.100 to 100.000)
*  -rewriteformat      menu       [p] Output format (Values: p (PHYLIP); n
                                  (NEXUS); x (XML))
*  -blocksize          integer    [1] Block size for bootstraping (Integer 1
                                  or more)
*  -reps               integer    [100] How many replicates (Integer 1 or
                                  more)
*  -justweights        menu       [d] Write out datasets or just weights
                                  (Values: d (Datasets); w (Weights))
   -enzymes            boolean    [N] Is the number of enzymes present in
                                  input file
*  -seed               integer    [1] Random number seed between 1 and 32767
                                  (must be odd) (Integer from 1 to 32767)
   -printdata          boolean    [N] Print out the data at start of run
*  -[no]dotdiff        boolean    [Y] Use dot-differencing
   -[no]progress       boolean    [Y] Print indications of progress of run

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-infile]
(Parameter 1) discretestates File containing one or more sets of restriction data Discrete states file

[-outfile]
(Parameter 2) outfile Phylip seqboot_rest program output file Output file <*>.frestboot

Additional (Optional) qualifiers

-weights properties Weights file Property value(s)

-test list Choose test
b (Bootstrap)
j (Jackknife)
c (Permute species for each character)
o (Permute character order)
s (Permute within species)
r (Rewrite data)
b

-regular toggle Altered sampling fraction Toggle value Yes/No No

-fracsample float Samples as percentage of sites Number from 0.100 to 100.000 100.0

-rewriteformat list Output format
p (PHYLIP)
n (NEXUS)
x (XML)
p

-blocksize integer Block size for bootstraping Integer 1 or more 1

-reps integer How many replicates Integer 1 or more 100

-justweights list Write out datasets or just weights
d (Datasets)
w (Weights)
d

-enzymes boolean Is the number of enzymes present in input file Boolean value Yes/No No

-seed integer Random number seed between 1 and 32767 (must be odd) Integer from 1 to 32767 1

-printdata boolean Print out the data at start of run Boolean value Yes/No No

-[no]dotdiff boolean Use dot-differencing Boolean value Yes/No Yes

-[no]progress boolean Print indications of progress of run Boolean value Yes/No Yes

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-outfile" associated outfile qualifiers

-odirectory2
-odirectory_outfile string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

Input file format

frestboot 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 programsreads any normal sequence USAs.

Input files for usage example

File: restboot.dat

   5   13   2
Alpha     ++-+-++--+++-
Beta      ++++--+--+++-
Gamma     -+--+-++-+-++
Delta     ++-+----++---
Epsilon   ++++----++---

Output file format

frestboot output 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 Factors option causes the characters to be resampled together. If (say) three adjacent characters all have the same factors characters, so that they all are understood to be recoding one multistate character, they will be resampled together as a group.

The order of species in the data sets in the output file will vary randomly. This is a precaution to help the programs that analyze these data avoid any result which is sensitive to the input order of species from showing up repeatedly and thus appearing to have evidence in its favor.

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 a 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.

Output files for usage example

File: restboot.frestboot

    5    13
Alpha     +--++-+++- -++
Beta      +++++----- -++
Gamma     -----+---+ +++
Delta     +--++----- -+-
Epsilon   +++++----- -+-
    5    13
Alpha     ++----+++- +++
Beta      +++-----+- +++
Gamma     -+-+++--++ ++-
Delta     ++-------- ++-
Epsilon   +++------- ++-
    5    13
Alpha     ++++++-+++ ---
Beta      ++++++-+++ ---
Gamma     --++-++--- +++
Delta     +++++----- ---
Epsilon   +++++----- ---
    5    13
Alpha     ++++-+++++ ---
Beta      ++-+-+++++ ---
Gamma     ---+-++--- +++
Delta     ++--+++--- ---
Epsilon   ++--+++--- ---
    5    13
Alpha     +-+++-++++ +--
Beta      +++++-++++ +--
Gamma     ----+----- +++
Delta     +-++-+---- ---
Epsilon   ++++-+---- ---
    5    13
Alpha     +++------- +++
Beta      +++------- +++
Gamma     +--++++++- +-+
Delta     +++------+ +--
Epsilon   +++------+ +--
    5    13
Alpha     ++++-+--++ ++-
Beta      ++++----++ ++-
Gamma     --+++---+- -++
Delta     ++++--+++- ---
Epsilon   ++++--+++- ---
    5    13
Alpha     +--+---+++ +--
Beta      ++++---+++ +--
Gamma     ----++-+-+ +++
Delta     +--+--++-- ---
Epsilon   ++++--++-- ---
    5    13
Alpha     +++--++--+ ++-


  [Part of this file has been deleted for brevity]

Gamma     -+--++-+++ -++
Delta     ++++------ +++
Epsilon   ++++------ +++
    5    13
Alpha     +++---+-++ +++
Beta      +++---+-++ +++
Gamma     ---++++-++ -++
Delta     +++----+++ ---
Epsilon   +++----+++ ---
    5    13
Alpha     ++++--+--+ +--
Beta      +++++----+ +--
Gamma     ---+-+-+++ +++
Delta     ++++-----+ +--
Epsilon   +++++----+ +--
    5    13
Alpha     +-----+--- +++
Beta      +++++++--- +++
Gamma     +------+++ +--
Delta     +-----+--- +--
Epsilon   +++++++--- +--
    5    13
Alpha     +-++--+-++ +--
Beta      ++++--+-++ +--
Gamma     +---++++-- -++
Delta     +-++------ ---
Epsilon   ++++------ ---
    5    13
Alpha     +++-+-++++ ++-
Beta      +++---++++ ++-
Gamma     --++--++-- +++
Delta     +++--+++-- ---
Epsilon   +++--+++-- ---
    5    13
Alpha     ++-+++--++ +--
Beta      +++-++--++ +--
Gamma     ----+++--- +++
Delta     ++-----+-- ---
Epsilon   +++----+-- ---
    5    13
Alpha     +---++---- ++-
Beta      ++---+---- ++-
Gamma     --++-+---- -++
Delta     +-----++++ ---
Epsilon   ++----++++ ---
    5    13
Alpha     +++-++++-+ +++
Beta      +++++----+ +++
Gamma     -++------+ +++
Delta     +++-+---++ ---
Epsilon   +++++---++ ---

Data files

None

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
distmat	Create a distance matrix from a multiple sequence alignment
ednacomp	DNA compatibility algorithm
ednadist	Nucleic acid sequence distance matrix program
ednainvar	Nucleic acid sequence invariants method
ednaml	Phylogenies from nucleic acid maximum likelihood
ednamlk	Phylogenies from nucleic acid maximum likelihood with clock
ednapars	DNA parsimony algorithm
ednapenny	Penny algorithm for DNA
eprotdist	Protein distance algorithm
eprotpars	Protein parsimony algorithm
erestml	Restriction site maximum likelihood method
eseqboot	Bootstrapped sequences algorithm
fdiscboot	Bootstrapped discrete sites algorithm
fdnacomp	DNA compatibility algorithm
fdnadist	Nucleic acid sequence distance matrix program
fdnainvar	Nucleic acid sequence invariants method
fdnaml	Estimate nucleotide phylogeny by maximum likelihood
fdnamlk	Estimates nucleotide phylogeny by maximum likelihood
fdnamove	Interactive DNA parsimony
fdnapars	DNA parsimony algorithm
fdnapenny	Penny algorithm for DNA
fdolmove	Interactive Dollo or polymorphism parsimony
ffreqboot	Bootstrapped genetic frequencies algorithm
fproml	Protein phylogeny by maximum likelihood
fpromlk	Protein phylogeny by maximum likelihood
fprotdist	Protein distance algorithm
fprotpars	Protein parsimony algorithm
frestdist	Calculate distance matrix from restriction sites or fragments
frestml	Restriction site maximum likelihood method
fseqboot	Bootstrapped sequences algorithm
fseqbootall	Bootstrapped sequences algorithm

Author(s)

This program is an EMBOSS conversion of a program written by Joe Felsenstein as part of his PHYLIP package.

History

Written (2004) - Joe Felsenstein, University of Washington.

Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: restboot.dat

Output file format

Output files for usage example

File: restboot.frestboot

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments