YN00 version 0.01

NAME

Module Name : YN00

INSTALLATION

To install this module type the following:

perl Makefile.PL
make
make test
make install

DEPENDENCIES

C compiler

SYNOPSIS

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

DESCRIPTION

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 same:

      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.

CAVEATS / LIMITATIONS

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

COPYRIGHT AND LICENCE

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.