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eseqboot |
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% eseqboot
Bootstrapped sequences algorithm
Phylip seqboot program input file: seqboot.dat
Random number seed (must be odd) [3]:
Method
Seq : Molecular sequences
Mor : Discrete Morphology
Res : Restriction Sites
Gen : Gene Frequencies
Choose the method [Seq]:
test
Boot : Bootstrap
Jack : Delete-half Jackknife
Perm : Permute species for each character
Choose test [Boot]:
How many replicates [100]:
Phylip seqboot program output file [eseqboot.outfile]:
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Go to the input files for this example
Go to the output files for this example
Bootstrapped sequences algorithm
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-datafile] infile Phylip seqboot program input file
-randseed integer [3] Random number seed (must be odd) (Any
integer value)
-method menu [Seq] Choose the method (Values: Seq
(Molecular sequences); Mor (Discrete
Morphology); Res (Restriction Sites); Gen
(Gene Frequencies))
-test menu [Boot] Choose test (Values: Boot
(Bootstrap); Jack (Delete-half Jackknife);
Perm (Permute species for each character))
-reps integer [100] How many replicates (Integer 1 or
more)
[-outfile] outfile [eseqboot.outfile] Phylip seqboot program
output file
Additional (Optional) qualifiers (* if not always prompted):
* -enzymes boolean [N] Present in input file
* -all boolean [N] All alleles present at each locus
-inter boolean [N] Interleaved input
-printdata boolean [N] Print out the data at start of run
-progress boolean [N] 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
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| Qualifier | Type | Description | Allowed values | Default | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||
| [-datafile] (Parameter 1) |
infile | Phylip seqboot program input file | Input file | Required | ||||||||
| -randseed | integer | Random number seed (must be odd) | Any integer value | 3 | ||||||||
| -method | list | Choose the method |
|
Seq | ||||||||
| -test | list | Choose test |
|
Boot | ||||||||
| -reps | integer | How many replicates | Integer 1 or more | 100 | ||||||||
| [-outfile] (Parameter 2) |
outfile | Phylip seqboot program output file | Output file | eseqboot.outfile | ||||||||
| Additional (Optional) qualifiers | ||||||||||||
| -enzymes | boolean | Present in input file | Boolean value Yes/No | No | ||||||||
| -all | boolean | All alleles present at each locus | Boolean value Yes/No | No | ||||||||
| -inter | boolean | Interleaved input | Boolean value Yes/No | No | ||||||||
| -printdata | boolean | Print out the data at start of run | Boolean value Yes/No | No | ||||||||
| -progress | boolean | Print indications of progress of run | Boolean value Yes/No | No | ||||||||
| 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 | ||||||||
5 6
Alpha AACAAC
Beta AACCCC
Gamma ACCAAC
Delta CCACCA
Epsilon CCAAAC
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5 6
Alpha AAAAAC
Beta AAAAAC
Gamma AAACCC
Delta CCCCCA
Epsilon CCCCCC
5 6
Alpha AAACAA
Beta AAACCC
Gamma ACCCAA
Delta CCCACC
Epsilon CCCAAA
5 6
Alpha ACCACC
Beta ACCCCC
Gamma ACCACC
Delta CAACAA
Epsilon CAAACC
5 6
Alpha AAAAAC
Beta AAACCC
Gamma AACAAC
Delta CCCCCA
Epsilon CCCAAC
5 6
Alpha AACCAC
Beta AACCCC
Gamma CCCCAC
Delta CCAACA
Epsilon CCAAAC
5 6
Alpha ACAAAC
Beta ACCCCC
Gamma CCAAAC
Delta CACCCA
Epsilon CAAAAC
5 6
Alpha ACCAAA
Beta ACCCCC
Gamma CCCAAA
Delta CAACCC
Epsilon CAAAAA
5 6
Alpha AAAAAC
Beta AACCCC
Gamma CCAAAC
Delta CCCCCA
Epsilon CCAAAC
5 6
Alpha AACAAC
[Part of this file has been deleted for brevity]
Gamma ACCCAC
Delta CCAACA
Epsilon CCAAAC
5 6
Alpha CAAAAC
Beta CCCCCC
Gamma CAAAAC
Delta ACCCCA
Epsilon AAAAAC
5 6
Alpha AAACCC
Beta AAACCC
Gamma AACCCC
Delta CCCAAA
Epsilon CCCACC
5 6
Alpha AACACC
Beta AACCCC
Gamma AACACC
Delta CCACAA
Epsilon CCAACC
5 6
Alpha AAAACC
Beta AAAACC
Gamma AACCCC
Delta CCCCAA
Epsilon CCCCAA
5 6
Alpha AAACAA
Beta AAACCC
Gamma AACCAA
Delta CCCACC
Epsilon CCCAAA
5 6
Alpha AACAAC
Beta AACCCC
Gamma ACCAAC
Delta CCACCA
Epsilon CCAAAC
5 6
Alpha AACACC
Beta AACCCC
Gamma AACACC
Delta CCACAA
Epsilon CCAACC
5 6
Alpha AAACAC
Beta AAACCC
Gamma CCCCAC
Delta CCCACA
Epsilon CCCAAC
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| 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 |
| 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 |
| 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 |
This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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