frestdist.txt

emboss的linux版本的源代码

   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-data]
   (Parameter 1) File containing one or more sets of restriction data
   Discrete states file
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.frestdist
   Additional (Optional) qualifiers Allowed values Default
   -[no]restsites Restriction sites (put N if you want restriction
   fragments) Boolean value Yes/No Yes
   -neili Use original Nei/Li model (default uses modified Nei/Li model)
   Boolean value Yes/No No
   -gamma Gama distributed rates among sites Boolean value Yes/No No
   -gammacoefficient Coefficient of variation of substitution rate among
   sites Number 0.001 or more 1
   -ttratio Transition/transversion ratio Number 0.001 or more 2.0
   -sitelength Site length Integer 1 or more 6
   -lower Lower triangular distance matrix Boolean value Yes/No No
   -printdata Print data at start of run Boolean value Yes/No No
   -[no]progress Print indications of progress of run Boolean value
   Yes/No Yes
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   frestdist input is fairly standard, with one addition. As usual the
   first line of the file gives the number of species and the number of
   sites, but there is also a third number, which is the number of
   different restriction enzymes that were used to detect the restriction
   sites. Thus a data set with 10 species and 35 different sites,
   representing digestion with 4 different enzymes, would have the first
   line of the data file look like this:

   10   35    4

   The site data are in standard form. Each species starts with a species
   name whose maximum length is given by the constant "nmlngth" (whose
   value in the program as distributed is 10 characters). The name
   should, as usual, be padded out to that length with blanks if
   necessary. The sites data then follows, one character per site (any
   blanks will be skipped and ignored). Like the DNA and protein sequence
   data, the restriction sites data may be either in the "interleaved"
   form or the "sequential" form. Note that if you are analyzing
   restriction sites data with the programs DOLLOP or MIX or other
   discrete character programs, at the moment those programs do not use
   the "aligned" or "interleaved" data format. Therefore you may want to
   avoid that format when you have restriction sites data that you will
   want to feed into those programs.

   The presence of a site is indicated by a "+" and the absence by a "-".
   I have also allowed the use of "1" and "0" as synonyms for "+" and
   "-", for compatibility with MIX and DOLLOP which do not allow "+" and
   "-". If the presence of the site is unknown (for example, if the DNA
   containing it has been deleted so that one does not know whether it
   would have contained the site) then the state "?" can be used to
   indicate that the state of this site is unknown.

  Input files for usage example

  File: restdist.dat

   5   13   2
Alpha     ++-+-++--+++-
Beta      ++++--+--+++-
Gamma     -+--+-++-+-++
Delta     ++-+----++---
Epsilon   ++++----++---

Output file format

   frestdist output contains on its first line the number of species. The
   distance matrix is then printed in standard form, with each species
   starting on a new line with the species name, followed by the
   distances to the species in order. These continue onto a new line
   after every nine distances. If the L option is used, the matrix or
   distances is in lower triangular form, so that only the distances to
   the other species that precede each species are printed. Otherwise the
   distance matrix is square with zero distances on the diagonal. In
   general the format of the distance matrix is such that it can serve as
   input to any of the distance matrix programs.

   If the option to print out the data is selected, the output file will
   precede the data by more complete information on the input and the
   menu selections. The output file begins by giving the number of
   species and the number of characters.

   The distances printed out are scaled in terms of expected numbers of
   substitutions per DNA site, counting both transitions and
   transversions but not replacements of a base by itself, and scaled so
   that the average rate of change, averaged over all sites analyzed, is
   set to 1.0. Thus when the G option is used, the rate of change at one
   site may be higher than at another, but their mean is expected to be
   1.

  Output files for usage example

  File: restdist.frestdist

    5
Alpha       0.000000  0.022368  0.107681  0.068767  0.082639
Beta        0.022368  0.000000  0.107681  0.068767  0.044216
Gamma       0.107681  0.107681  0.000000  0.176484  0.192466
Delta       0.068767  0.068767  0.176484  0.000000  0.019724
Epsilon     0.082639  0.044216  0.192466  0.019724  0.000000

Data files

   None

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                         Description
   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 pasimony algorithm
   frestboot    Bootstrapped restriction sites algorithm
   frestml      Restriction site maximum Likelihood method
   fseqboot     Bootstrapped sequences algorithm
   fseqbootall  Bootstrapped sequences algorithm

Author(s)

   This program is an EMBOSS conversion of a program written by Joe
   Felsenstein as part of his PHYLIP package.

   Although we take every care to ensure that the results of the EMBOSS
   version are identical to those from the original package, we recommend
   that you check your inputs give the same results in both versions
   before publication.

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   not to the original author.

History

   Written (2004) - Joe Felsenstein, University of Washington.

   Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.