                                   frestml



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Restriction site maximum Likelihood method

Description

   Estimation of phylogenies by maximum likelihood using restriction sites
   data (not restriction fragments but presence/absence of individual
   sites). It employs the Jukes-Cantor symmetrical model of nucleotide
   change, which does not allow for differences of rate between
   transitions and transversions. This program is very slow.

Algorithm

   This program implements a maximum likelihood method for restriction
   sites data (not restriction fragment data). This program is one of the
   slowest programs in this package, and can be very tedious to run. It is
   possible to have the program search for the maximum likelihood tree. It
   will be more practical for some users (those that do not have fast
   machines) to use the U (User Tree) option, which takes less run time,
   optimizing branch lengths and computing likelihoods for particular tree
   topologies suggested by the user. The model used here is essentially
   identical to that used by Smouse and Li (1987) who give explicit
   expressions for computing the likelihood for three-species trees. It
   does not place prior probabilities on trees as they do. The present
   program extends their approach to multiple species by a technique
   which, while it does not give explicit expressions for likelihoods,
   does enable their computation and the iterative improvement of branch
   lengths. It also allows for multiple restriction enzymes. The algorithm
   has been described in a paper (Felsenstein, 1992). Another relevant
   paper is that of DeBry and Slade (1985).

   The assumptions of the present model are:
    1. Each restriction site evolves independently.
    2. Different lineages evolve independently.
    3. Each site undergoes substitution at an expected rate which we
       specify.
    4. Substitutions consist of replacement of a nucleotide by one of the
       other three nucleotides, chosen at random.

   Note that if the existing base is, say, an A, the chance of it being
   replaced by a G is 1/3, and so is the chance that it is replaced by a
   T. This means that there can be no difference in the (expected) rate of
   transitions and transversions. Users who are upset at this might ponder
   the fact that a version allowing different rates of transitions and
   transversions would run an estimated 16 times slower. If it also
   allowed for unequal frequencies of the four bases, it would run about
   300,000 times slower! For the moment, until a better method is
   available, I guess I'll stick with this one!

   Subject to these assumptions, the program is an approximately correct
   maximum likelihood method.

Usage

   Here is a sample session with frestml


% frestml
Restriction site maximum Likelihood method
Input file: restml.dat
Phylip tree file (optional):
Phylip restml program output file [restml.frestml]:

numseqs: 1

Adding species:
   1. Alpha
   2. Beta
   3. Gamma
   4. Delta
   5. Epsilon

Output written to file "restml.frestml"

Tree also written onto file "restml.treefile"

Done.



   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Restriction site maximum Likelihood method
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-data]              discretestates File containing one or more sets of
                                  restriction data
  [-intreefile]        tree       Phylip tree file (optional)
  [-outfile]           outfile    [*.frestml] Phylip restml program output
                                  file

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -njumble            integer    [0] Number of times to randomise (Integer 0
                                  or more)
*  -seed               integer    [1] Random number seed between 1 and 32767
                                  (must be odd) (Integer from 1 to 32767)
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -[no]allsites       boolean    [Y] All sites detected
*  -lengths            boolean    [N] Use lengths from user trees
   -sitelength         integer    [6] Site length (Integer from 1 to 8)
*  -global             boolean    [N] Global rearrangements
*  -[no]rough          boolean    [Y] Speedier but rougher analysis
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.frestml] Phylip tree output file
   -printdata          boolean    [N] Print data at start of run
   -[no]progress       boolean    [Y] Print indications of progress of run
   -[no]treeprint      boolean    [Y] Print out tree

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory3        string     Output directory

   "-outtreefile" associated qualifiers
   -odirectory         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


Input file format

   frestml 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 first line of the data file will also contain a letter W following
   these numbers (and separated from them by a space) if the Weights
   option is being used. As with all programs using the weights option, a
   line or lines must then follow, before the data, with the weights for
   each site.

   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.

   User-defined trees may follow the data in the usual way. The trees must
   be unrooted, which means that at their base they must have a
   trifurcation.

  Input files for usage example

  File: restml.dat

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

Output file format

   frestml outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

  Output files for usage example

  File: restml.frestml


Restriction site Maximum Likelihood method, version 3.69


  Recognition sequences all 6 bases long

Sites absent from all species are assumed to have been omitted




  +----Gamma
  |
  |  +Beta
  1--2
  |  |  +Epsilon
  |  +--3
  |     +Delta
  |
  +Alpha


remember: this is an unrooted tree!

Ln Likelihood =   -40.47082


 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------
   1          Gamma           0.10794     (  0.01144,     0.21872) **
   1             2            0.01244     (     zero,     0.04712)
   2          Beta            0.00100     (     zero,    infinity)
   2             3            0.05878     (     zero,     0.12675) **
   3          Epsilon         0.00022     (     zero,    infinity)
   3          Delta           0.01451     (     zero,     0.04459) **
   1          Alpha           0.01244     (     zero,     0.04717)

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01



  File: restml.treefile

(Gamma:0.10794,(Beta:0.00100,(Epsilon:0.00022,
Delta:0.01451):0.05878):0.01244,Alpha:0.01244);

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
                    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
                    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.
