Beefy Boxes and Bandwidth Generously Provided by pair Networks
go ahead... be a heretic
 
PerlMonks  

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??


in reply to Re^2: phylogenetic tree construction using perl
in thread phylogenetic tree construction using perl

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.

By the way, your link to your jpeg on picpaste doesn't display anything.

  • Comment on Re^3: phylogenetic tree construction using perl

Replies are listed 'Best First'.
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
    Hi jgamble, Did you get the algorithm. Please help me on it. http://picpaste.com/Z1SVFTT6.png

    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.

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://996063]
help
Chatterbox?
[Marshall]: stevieb wish you well with water problems, my water was off all day Monday for repairs. Any more progress on .exe info problem?.
[stevieb]: Marshall: no. I commented on the thread yesterday. Visual Studio updates the tags ok, but corrupts the exe
[stevieb]: I advised the OP that a possible workaround would be to add a version function/flag that displays the required copyright/license info instead
[Marshall]: Darn! I'll look at the thread. Must not be updatinga byte count somewhere. The .exe format is a complex critter.
[stevieb]: that way, it's still "hard coded" into the exe at least, despite not being visible via Properties
[Marshall]: I also looked into PerlApp from Active State, but they don't sell their Dev Kit independent of a very expensive ($1,200) per year license anymore.
[Corion]: I would assume that the PE format hasn't changed that much since the days of yore, but it seems that I would be wrong in that assumption
[Marshall]: When I bought my copy 15+ years ago, it was just a couple hundred bucks.

How do I use this? | Other CB clients
Other Users?
Others scrutinizing the Monastery: (11)
As of 2016-12-08 18:16 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?
    On a regular basis, I'm most likely to spy upon:













    Results (144 votes). Check out past polls.