Delila Program: aran

aran program

Documentation for the aran program is below, with links to related programs in the "see also" section.

{version = 1.16; (* of aran.p 1994 Sep 5}

(* begin module describe.aran *)
(*
name
   aran: aligned random sequences

synopsis
   aran(book: in, aranp: in, list: out, sequ: out, output: out)

files
   book: the book generated by Delila

   aranp:  Parameters to control the program.
      The FIRST LINE must contain one real number which is the degree of
      conservation.  For example, if this is 0.85, then each base will have 85%
      chance of being the same, while the other bases will be 5% each.

      The SECOND LINE must contain the number of sequences to generate.

   list: details of the run.

   sequ: the aligned sequences, for input to makebk

   output: messages to the user

description
   Aran takes a sequence as a starting point and generates random
   sequences from it.  The program simulates a very simple dirty synthesis of
   the sequence.  The synthesis is to be mostly the bases given in the
   sequence.  The probability of conserving each base (f) is defined in the
   parameter file.  If a particular base is not conserved, then the other
   three bases are assigned probabilities of (1-f)/3.

documentation
   delman.use.aligned.books

see also
   alist.p

author
   Thomas D. Schneider

bugs
   See alist

technical notes
   The program constant seqmax defines the length of the longest sequence
   that can be created.

*)
(* end module describe.aran *)
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