frestdist.txt

emboss的linux版本的源代码

                                 frestdist 



Function

   Distance matrix from restriction sites or fragments

Description

   Distances calculated from restriction sites data or restriction
   fragments data. The restriction sites option is the one to use to also
   make distances for RAPDs or AFLPs.

Algorithm

   Restdist reads the same restriction sites format as RESTML and
   computes a restriction sites distance. It can also compute a
   restriction fragments distance. The original restriction fragments and
   restriction sites distance methods were introduced by Nei and Li
   (1979). Their original method for restriction fragments is also
   available in this program, although its default methods are my
   modifications of the original Nei and Li methods.

   These two distances assume that the restriction sites are accidental
   byproducts of random change of nucleotide sequences. For my
   restriction sites distance the DNA sequences are assumed to be
   changing according to the Kimura 2-parameter model of DNA change
   (Kimura, 1980). The user can set the transition/transversion rate for
   the model. For my restriction fragments distance there is there is an
   implicit assumption of a Jukes-Cantor (1969) model of change, The user
   can also set the parameter of a correction for unequal rates of
   evolution between sites in the DNA sequences, using a Gamma
   distribution of rates among sites. The Jukes-Cantor model is also
   implicit in the restriction fragments distance of Nei and Li(1979). It
   does not allow us to correct for a Gamma distribution of rates among
   sites.

  Restriction Sites Distance

   The restriction sites distances use data coded for the presence of
   absence of individual restriction sites (usually as + and - or 0 and
   1). My distance is based on the proportion, out of all sites observed
   in one species or the other, which are present in both species. This
   is done to correct for the ascertainment of sites, for the fact that
   we are not aware of many sites because they do not appear in any
   species.

   My distance starts by computing from the particular pair of species
   the fraction

                 n++
   f =  ---------------------
         n++ + 1/2 (n+- + n-+)

   where n++ is the number of sites contained in both species, n+- is the
   number of sites contained in the first of the two species but not in
   the second, and n-+ is the number of sites contained in the second of
   the two species but not in the first. This is the fraction of sites
   that are present in one species which are present in both. Since the
   number of sites present in the two species will often differ, the
   denominator is the average of the number of sites found in the two
   species.

   If each restriction site is s nucleotides long, the probability that a
   restriction site is present in the other species, given that it is
   present in a species, is

      Qs,

   `where Q is the probability that a nucleotide has no net change as one
   goes from the one species to the other. It may have changed in
   between; we are interested in the probability that that nucleotide
   site is in the same base in both species, irrespective of what has
   happened in between. The distance is then computed by finding the
   branch length of a two-species tree (connecting these two species with
   a single branch) such that Q equals the s-th root of f. For this the
   program computes Q for various values of branch length, iterating them
   by a Newton-Raphson algorithm until the two quantities are equal.

   The resulting distance should be numerically close to the original
   restriction sites distance of Nei and Li (1979) when divergence is
   small. Theirs computes the probability of retention of a site in a way
   that assumes that the site is present in the common ancestor of the
   two species. Ours does not make this assumption. It is inspired by
   theirs, but differs in this detail. Their distance also assumes a
   Jukes-Cantor (1969) model of base change, and does not allow for
   transitions being more frequent than transversions. In this sense mine
   generalizes theres somewhat. Their distance does include, as mine does
   as well, a correction for Gamma distribution of rate of change among
   nucleotide sites.

   I have made their original distance available here

  Restriction Fragments Distance

   For restriction fragments data we use a different distance. If we
   average over all restriction fragment lengths, each at its own
   expected frequency, the probability that the fragment will still be in
   existence after a certain amount of branch length, we must take into
   account the probability that the two restriction sites at the ends of
   the fragment do not mutate, and the probability that no new
   restriction site occurs within the fragment in that amount of branch
   length. The result for a restriction site length of s is:

                Q2s
          f = --------
               2 - Qs

   (The details of the derivation will be given in my forthcoming book
   Inferring Phylogenies (to be published by Sinauer Associates in 2001).
   Given the observed fraction of restriction sites retained, f, we can
   solve a quadratic equation from the above expression for Qs. That
   makes it easy to obtain a value of Q, and the branch length can then
   be estimated by adjusting it so the probability of a base not changing
   is equal to that value. Alternatively, if we use the Nei and Li (1979)
   restriction fragments distance, this involves solving for g in the
   nonlinear equation

       g  =  [ f (3 - 2g) ]1/4

   and then the distance is given by

       d  =  - (2/r) loge(g)

   where r is the length of the restriction site.

   Comparing these two restriction fragments distances in a case where
   their underlying DNA model is the same (which is when the
   transition/transversion ratio of the modified model is set to 0.5),
   you will find that they are very close to each other, differing very
   little at small distances, with the modified distance become smaller
   than the Nei/Li distance at larger distances. It will therefore matter
   very little which one you use.

  A Comment About RAPDs and AFLPs

   Although these distances are designed for restriction sites and
   restriction fragments data, they can be applied to RAPD and AFLP data
   as well. RAPD (Randomly Amplified Polymorphic DNA) and AFLP (Amplified
   Fragment Length Polymorphism) data consist of presence or absence of
   individual bands on a gel. The bands are segments of DNA with PCR
   primers at each end. These primers are defined sequences of known
   length (often about 10 nucleotides each). For AFLPs the reolevant
   length is the primer length, plus three nucleotides. Mutation in these
   sequences makes them no longer be primers, just as in the case of
   restriction sites. Thus a pair of 10-nucleotide primers will behave
   much the same as a 20-nucleotide restriction site, for RAPDs (26 for
   AFLPs). You can use the restriction sites distance as the distance
   between RAPD or AFLP patterns if you set the proper value for the
   total length of the site to the total length of the primers (plus 6 in
   the case of AFLPs). Of course there are many possible sources of noise
   in these data, including confusing fragments of similar length for
   each other and having primers near each other in the genome, and these
   are not taken into account in the statistical model used here.

Usage

   Here is a sample session with frestdist


% frestdist 
Distance matrix from restriction sites or fragments
Input file: restdist.dat
Output file [restdist.frestdist]: 


Restriction site or fragment distances, version 3.6b

Distances calculated for species
    Alpha        ....
    Beta         ...
    Gamma        ..
    Delta        .
    Epsilon

Distances written to file "restdist.frestdist"

Done.


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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-data]              discretestates File containing one or more sets of
                                  restriction data
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers (* if not always prompted):
   -[no]restsites      boolean    Restriction sites (put N if you want
                                  restriction fragments)
   -neili              boolean    Use original Nei/Li model (default uses
                                  modified Nei/Li model)
*  -gamma              boolean    Gama distributed rates among sites
*  -gammacoefficient   float      Coefficient of variation of substitution
                                  rate among sites
   -ttratio            float      Transition/transversion ratio
   -sitelength         integer    Site length
   -lower              boolean    Lower triangular distance matrix
   -printdata          boolean    Print data at start of run
   -[no]progress       boolean    Print indications of progress of run

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

   "-outfile" associated qualifiers