YN00 version 0.01

   Module Name : YN00 


To install this module type the following:

   perl Makefile.PL
   make test
   make install


   C compiler


   use YN00;
   @arg = ($filename,$,$,$);
   $ref_ary = YN00::cal_kaks(\@arg);
   @kaks_values = @{$ref_ary};


   This is a module that uses SWIG to make PAML/yn00.c usable in Perl. It
   does not parse output file(s) originally generated by PAML/yn00.c. Actually
   there is no output file at all. The argument users need to provide is the
      sequence file: containing aligned DNA sequences;
      icode: genetic codes (0..10)
         0 - universal code, 
	 1 - mammalian mt,
	 2 - yeast mt.,
	 3 - mold mt.,
	 4 - invertebrate mt.,
	 5 - ciliate nuclear,
	 6 - echinoderm mt.,
	 7 - euplotid mt.,
	 8 - alternative yeast nu.,
	 9 - ascidian mt.,
	 10 - blepharisma nu.
      weighting: weighting pathways between codons (0/1)
      commonf3x4: use one set of codon freqs for all pairs (0/1)
   For two sequences, the module will calculate the Ka and ks values based
   on Yang et all 2000 paper algorithm. It returns 6 values accordingly:
   S : number of synonymous site.
   N : number of non-synonymous site.
   dN : the number of non-synonymous changes per non-synonymous site. 
   SE : standard deviation of dN
   dS : the number of synonymous changes per synonymous site.
   SE : standard deviation of dS
   If there are more than two sequences, the values will be appended at the
   end of array accordingly.
   This is created from paml3.13 version.


   1. Input sequence file must fit the requirement of PAML/yn00.c
      Ex. Sequence length must be multiple of three
          No stop codon is allowed.
   2. If something wrong is happened, the module will exit the program.


Copyright (C) 2004 by Wen-Yu Chung <wychung@psu.edu>.

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.3 or,
at your option, any later version of Perl 5 you may have available.