fdiscboot |
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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]: 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. |
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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 |
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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 |
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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 | 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 |
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