EMBOSS: eseqboot

eseqboot

Function

Conversion of PHYLIP's seqboot

Description

ESEQBOOT -- Bootstrap, Jackknife, or Permutation Resampling of Molecular Sequence, Restriction Site, Gene Frequency or Character Data

Phylip seqboot documentation.

Usage

Here is a sample session with eseqboot using the data below and replicates are set to 10 and seed to 4331

    5    6
Alpha     AACAAC
Beta      AACCCC
Gamma     ACCAAC
Delta     CCACCA
Epsilon   CCAAAC


% eseqboot test

Bootstrapped sequences algorithm
Output file [eseqboot.outfile]: stdout
Random number seed (must be odd) [3]: 4331
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]: 10
    5     6
Alpha        ACCCAC
Beta         ACCCCC
Gamma        CCCCAC
Delta        CAAACA
Epsilon      CAAAAC
    5     6
Alpha        AAAACC
Beta         AACCCC
Gamma        ACAACC
Delta        CCCCAA
Epsilon      CCAACC
    5     6
Alpha        AAAAAC
Beta         AACCCC
Gamma        CCAAAC
Delta        CCCCCA
Epsilon      CCAAAC
    5     6
Alpha        AAAAAA
Beta         AACCCC
Gamma        ACAAAA
Delta        CCCCCC
Epsilon      CCAAAA
    5     6
Alpha        ACCCAA
Beta         ACCCCC
Gamma        CCCCAA
Delta        CAAACC
Epsilon      CAAAAA
    5     6
Alpha        AAACCC
Beta         AAACCC
Gamma        AACCCC
Delta        CCCAAA
Epsilon      CCCACC
    5     6
Alpha        AACAAC
Beta         AACCCC
Gamma        ACCAAC
Delta        CCACCA
Epsilon      CCAAAC
    5     6
Alpha        ACCCAA
Beta         ACCCCC
Gamma        ACCCAA
Delta        CAAACC
Epsilon      CAAAAA
    5     6
Alpha        AACACC
Beta         AACCCC
Gamma        ACCACC
Delta        CCACAA
Epsilon      CCAACC
    5     6
Alpha        AAAACA
Beta         AAAACC
Gamma        AAAACA
Delta        CCCCAC
Epsilon      CCCCAA

Command line arguments

   Mandatory qualifiers:
  [-datafile]          infile     Input file
  [-outfile]           outfile    Output file name
   -randseed           integer    Random number seed (must be odd)
   -method             list       Choose the method
   -test               list       Choose test
   -reps               integer    How many replicates

   Optional qualifiers (* if not always prompted):
   -inter              bool       Interleaved input
*  -enzymes            bool       Present in input file
*  -all                bool       All alleles present at each locus
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default

[-datafile]
(Parameter 1) Input file Input file Required

[-outfile]
(Parameter 2) Output file name Output file eseqboot.outfile

-randseed Random number seed (must be odd) Any integer value 3

-method Choose the method
Seq (Molecular sequences)
Mor (Discrete Morphology)
Res (Restriction Sites)
Gen (Gene Frequencies)
Seq

-test Choose test
Boot (Bootstrap)
Jack (Delete-half Jackknife)
Perm (Permute species for each character)
Boot

-reps How many replicates Integer 1 or more 100

Optional qualifiers Allowed values Default

-inter Interleaved input Yes/No No

-enzymes Present in input file Yes/No No

-all All alleles present at each locus Yes/No No

-printdata Print out the data at start of run Yes/No No

-progress Print indications of progress of run Yes/No No

Advanced qualifiers Allowed values Default

(none)

Data files

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

Author(s)

(c) Copyright 1991-1993 by the University of Washington and by Joseph Felsenstein. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

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.