So, if you use the fixes from the posts above, you should be able to output a minimum change in each base from the transcription factor binding site. In the top up phase it looks like you are clustering the individual bases to determine the sequence variability and relations in the sequence itself. By recursively clustering these, you should be able to output a second value that serves as a "score" for the sequence variation, which then allows you to cluster again in the top down version to determine the genotypic relation of the various species. A simple way to cluster them would be to use a sub to recursively find the difference of the "values" your getting for each base associated with each species, pushing them into an array, and them using them to create a second value which is then used to determine the larger phylogenetic tree. It would be more efficient to use a matrix to sort and output those values so that the changes would be more fluid and dynamic and use less memory, etc. Bioperl has a couple modules that are already made to determine the distances in the various nodes, so you could integrate these into your program to get the larger phylogenetic output you desire.

Check out Module:Bio::Tree::Node, as well as Module:Bio::Align::DNAStatistics, which if I recall can do something of what your trying to do above. Good luck!

Bioinformatics

In reply to Re: Maximal Parsimony Problem by bioinformatics
in thread Maximal Parsimony Problem by neversaint

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.