fseqboot |
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 |
% fseqboot -seed 3 Bootstrapped sequences algorithm Input (aligned) sequence set: seqboot.dat Phylip seqboot_seq program output file [seqboot.fseqboot]: 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 "seqboot.fseqboot" Done. |
Go to the input files for this example
Go to the output files for this example
Bootstrapped sequences algorithm Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqset (Aligned) sequence set filename and optional format, or reference (input USA) [-outfile] outfile [*.fseqboot] Phylip seqboot_seq program output file Additional (Optional) qualifiers (* if not always prompted): -categories properties File of input categories -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)) * -seqtype menu [d] Output format (Values: d (dna); p (protein); r (rna)) * -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: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-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 | ||||||||||||||||
[-sequence] (Parameter 1) |
seqset | (Aligned) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||||||||||
[-outfile] (Parameter 2) |
outfile | Phylip seqboot_seq program output file | Output file | <*>.fseqboot | ||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||
-categories | properties | File of input categories | Property value(s) | |||||||||||||
-weights | properties | Weights 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 | ||||||||||||
-rewriteformat | list | Output format |
|
p | ||||||||||||
-seqtype | list | Output format |
|
d | ||||||||||||
-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 | ||||||||||||||||
"-sequence" associated seqset qualifiers | ||||||||||||||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||||||||
-send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 | ||||||||||||
-sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||||||
-sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||||||
-snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||||||
-sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||||||
-slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||||||
-supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||||||
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||||||
-sdbname1 -sdbname_sequence |
string | Database name | Any string | |||||||||||||
-sid1 -sid_sequence |
string | Entryname | Any string | |||||||||||||
-ufo1 -ufo_sequence |
string | UFO features | Any string | |||||||||||||
-fformat1 -fformat_sequence |
string | Features format | Any string | |||||||||||||
-fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |||||||||||||
"-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 |
5 6 Alpha AACAAC Beta AACCCC Gamma ACCAAC Delta CCACCA Epsilon CCAAAC |
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.
5 6 Alpha AAACCA Beta AAACCC Gamma ACCCCA Delta CCCAAC Epsilon CCCAAA 5 6 Alpha AAACAA Beta AAACCC Gamma ACCCAA Delta CCCACC Epsilon CCCAAA 5 6 Alpha AAAAAC Beta AAACCC Gamma AACAAC Delta CCCCCA Epsilon CCCAAC 5 6 Alpha CCCCCA Beta CCCCCC Gamma CCCCCA Delta AAAAAC Epsilon AAAAAA 5 6 Alpha AAAACC Beta AAACCC Gamma AACACC Delta CCCCAA Epsilon CCCACC 5 6 Alpha AAAACC Beta ACCCCC Gamma AAAACC Delta CCCCAA Epsilon CAAACC 5 6 Alpha AACCAA Beta AACCCC Gamma ACCCAA Delta CCAACC Epsilon CCAAAA 5 6 Alpha AAAACC Beta ACCCCC Gamma AAAACC Delta CCCCAA Epsilon CAAACC 5 6 Alpha AACACC [Part of this file has been deleted for brevity] Gamma ACAAAA Delta CCCCCC Epsilon CCAAAA 5 6 Alpha AACAAC Beta AACCCC Gamma AACAAC Delta CCACCA Epsilon CCAAAC 5 6 Alpha AACAAA Beta AACCCC Gamma CCCAAA Delta CCACCC Epsilon CCAAAA 5 6 Alpha ACAAAA Beta ACCCCC Gamma CCAAAA Delta CACCCC Epsilon CAAAAA 5 6 Alpha CAAAAA Beta CCCCCC Gamma CAAAAA Delta ACCCCC Epsilon AAAAAA 5 6 Alpha CAACCC Beta CCCCCC Gamma CAACCC Delta ACCAAA Epsilon AAACCC 5 6 Alpha ACAACC Beta ACCCCC Gamma ACAACC Delta CACCAA Epsilon CAAACC 5 6 Alpha AAAAAA Beta AAAAAC Gamma ACCCCA Delta CCCCCC Epsilon CCCCCA 5 6 Alpha AACAAC Beta AACCCC Gamma CCCAAC Delta CCACCA Epsilon CCAAAC |
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 | 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 |
fseqbootall | Bootstrapped sequences algorithm |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.