fdiscboot

 

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Function

Bootstrapped discrete 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

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:

Usage

Here is a sample session with fdiscboot


% fdiscboot -seed 3 
Bootstrapped discrete sites algorithm
Input file: discboot.dat
Phylip seqboot_disc program output file [discboot.fdiscboot]: 
Phylip ancestor data output file (optional) [discboot.ancfile]: 
Phylip mix data output file (optional) [discboot.mixfile]: 
Phylip factor data output file (optional) [discboot.factfile]: 


 bootstrap: true
jackknife: false
 permute: false
 lockhart: false
 ild: false
 justwts: false 

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 "discboot.fdiscboot"

Done.


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

Command line arguments

Bootstrapped discrete sites algorithm
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            discretestates (no help text) discretestates value
  [-outfile]           outfile    [*.fdiscboot] Phylip seqboot_disc program
                                  output file
  [-outancfile]        outfile    [*.fdiscboot] Phylip ancestor data output
                                  file (optional)
  [-outmixfile]        outfile    [*.fdiscboot] Phylip mix data output file
                                  (optional)
  [-outfactfile]       outfile    [*.fdiscboot] Phylip factor data output file
                                  (optional)

   Additional (Optional) qualifiers (* if not always prompted):
   -mixfile            properties File of mixtures
   -ancfile            properties File of ancestors
   -weights            properties Weights file
   -factorfile         properties Factors 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)
*  -morphseqtype       menu       [p] Output format (Values: p (PHYLIP); n
                                  (NEXUS))
*  -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))
*  -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

   "-outancfile" associated qualifiers
   -odirectory3        string     Output directory

   "-outmixfile" associated qualifiers
   -odirectory4        string     Output directory

   "-outfactfile" associated qualifiers
   -odirectory5        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 (no help text) discretestates value Discrete states file  
[-outfile]
(Parameter 2)
outfile Phylip seqboot_disc program output file Output file <*>.fdiscboot
[-outancfile]
(Parameter 3)
outfile Phylip ancestor data output file (optional) Output file <*>.fdiscboot
[-outmixfile]
(Parameter 4)
outfile Phylip mix data output file (optional) Output file <*>.fdiscboot
[-outfactfile]
(Parameter 5)
outfile Phylip factor data output file (optional) Output file <*>.fdiscboot
Additional (Optional) qualifiers
-mixfile properties File of mixtures Property value(s)  
-ancfile properties File of ancestors Property value(s)  
-weights properties Weights file Property value(s)  
-factorfile properties Factors 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
-morphseqtype list Output format
p (PHYLIP)
n (NEXUS)
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
-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  
"-outancfile" associated outfile qualifiers
-odirectory3
-odirectory_outancfile
string Output directory Any string  
"-outmixfile" associated outfile qualifiers
-odirectory4
-odirectory_outmixfile
string Output directory Any string  
"-outfactfile" associated outfile qualifiers
-odirectory5
-odirectory_outfactfile
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

fdiscboot reads discrete character data

Input files for usage example

File: discboot.dat

     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110

Output file format

fdiscboot writes a bootstrap multiple set of discrete character data

Output files for usage example

File: discboot.ancfile


File: discboot.factfile


File: discboot.mixfile


File: discboot.fdiscboot

    5     6
Alpha     111001
Beta      111000
Gamma     100001
Delta     000110
Epsilon   000111
    5     6
Alpha     111011
Beta      111000
Gamma     100011
Delta     000100
Epsilon   000111
    5     6
Alpha     111110
Beta      111000
Gamma     110110
Delta     000001
Epsilon   000110
    5     6
Alpha     000001
Beta      000000
Gamma     000001
Delta     111110
Epsilon   111111
    5     6
Alpha     111100
Beta      111000
Gamma     110100
Delta     000011
Epsilon   000100
    5     6
Alpha     111100
Beta      100000
Gamma     111100
Delta     000011
Epsilon   011100
    5     6
Alpha     110011
Beta      110000
Gamma     100011
Delta     001100
Epsilon   001111
    5     6
Alpha     111100
Beta      100000
Gamma     111100
Delta     000011
Epsilon   011100
    5     6
Alpha     110100


  [Part of this file has been deleted for brevity]

Gamma     101111
Delta     000000
Epsilon   001111
    5     6
Alpha     110110
Beta      110000
Gamma     110110
Delta     001001
Epsilon   001110
    5     6
Alpha     110111
Beta      110000
Gamma     000111
Delta     001000
Epsilon   001111
    5     6
Alpha     101111
Beta      100000
Gamma     001111
Delta     010000
Epsilon   011111
    5     6
Alpha     011111
Beta      000000
Gamma     011111
Delta     100000
Epsilon   111111
    5     6
Alpha     011000
Beta      000000
Gamma     011000
Delta     100111
Epsilon   111000
    5     6
Alpha     101100
Beta      100000
Gamma     101100
Delta     010011
Epsilon   011100
    5     6
Alpha     111111
Beta      111110
Gamma     100001
Delta     000000
Epsilon   000001
    5     6
Alpha     110110
Beta      110000
Gamma     000110
Delta     001001
Epsilon   001110

Data files

None

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

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
fdnacomp DNA compatibility algorithm
fdnadist Nucleic acid sequence Distance Matrix program
fdnainvar Nucleic acid sequence Invariants method
fdnaml Estimates 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
frestboot Bootstrapped restriction sites algorithm
frestdist 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.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

None