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### Re^3: phylogenetic tree construction using perl

by jgamble (Pilgrim)
 on Sep 27, 2012 at 18:45 UTC ( #996063=note: print w/replies, xml ) Need Help??

I'm still reading through the Triplet Methods paper, so I'm certain my understanding is not only limited but wrong. Nonetheless, section 7.4.1 ("Reconstruct a network by a sorting network") caught my eye for the simple reason that Algorithm-Networksort exists on CPAN and I am its author.

So if the module can be of use to you, great. If there's a feature that you need from it that's doable, I'd be more than happy to add it to the module. Let me know.

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Re^4: phylogenetic tree construction using perl
by zing (Beadle) on Sep 27, 2012 at 19:13 UTC

Thanks for pointing it out jgamble. Actually the picpaste had figure 7.4 from the paper (which depicts the algorithm for a better understanding). And the algorithm is Alfred Aho's famous algorithm, which has been adopted by biologists to construct a tree. The problem is that it deals with connected components, subgraphs,recursion etc all at once. So Im having trouble proceeding, though im still trying to solve it moving in bits and pieces that is.

The algorithm TreeConstruct described in section 7.2.3 is my main concern.
Re^4: phylogenetic tree construction using perl
by zing (Beadle) on Sep 30, 2012 at 20:38 UTC

This is what a triplet looks like. The link below shows three triplets (a,b|c) (a,c|d) (d,e|b) and their consensus supertree. http://picpaste.com/Nu0ON9uo.jpg

I'm only able to look at the paper in my spare time, and I had no spare time for the past few days. Also, quite frankly, I didn't know if your problem had been solved already or not.

Did the bioperl suggestions lead anywhere for you?

I'll resume reading the paper tomorrow. If you have any further reading material that might be helpful, please let me know. I can be reached more directly at jgamble@cpan.org.

No Sir, Its not solved yet. Actually as previously wrote its the implementation of Alfred Aho's algorithm so as to construct a phylogenetic tree.The algorithm is there in section 7.2.3 of the paper. Sir thats the only material/paper Im following right now.

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