|   | fdiscboot | 
Please help by correcting and extending the Wiki pages.
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:
| 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 | 
| % 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]: 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
| 
Bootstrapped discrete sites algorithm
Version: EMBOSS:6.6.0.0
   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 | ||||||||||||
| -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 | ||||||||||||
| -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 | ||||||||||||
| -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 | ||||||||||||
| 
     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110
 | 
|  | 
|  | 
|  | 
| 
    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
 | 
| 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 | 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 | 
| frestboot | Bootstrapped restriction sites algorithm | 
| frestdist | Calculate distance matrix from restriction sites or fragments | 
| frestml | Restriction site maximum likelihood method | 
| fseqboot | Bootstrapped sequences algorithm | 
| fseqbootall | Bootstrapped sequences algorithm | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.