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Generalized Suffix Tree in Perl

by monkfan (Curate)
on Nov 23, 2005 at 09:23 UTC ( #511104=perlquestion: print w/replies, xml ) Need Help??

monkfan has asked for the wisdom of the Perl Monks concerning the following question:

Dear monks,
Does anybody knows if there exist any Perl implementation for generalized Suffix Tree?
What I can only find so far is Shlomo Yona`s module. Which is very limited and not a generalized one.

Update: Just discoverd there is a new module Tree::Suffix that binds to libstree library,
it takes care of generalized suffix tree.


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Re: Generalized Suffix Tree in Perl
by Happy-the-monk (Canon) on Nov 23, 2005 at 09:35 UTC

    ...Shlomo Yona`s module. Which is very limited...

    What functionality or generalisation are you particularly missing?

    Except from trying to contact Shlomo and maybe Offer and ask if they are interested or even into that kind of further development, I don't see anything that could help you right now. It seems the module wasn't meant to do what you need.

    Update 2:
    Further searching CPAN for "Tree" and "Trie" finds a bunch of modules. Maybe there's a more suitable alternative for you there?

    Cheers, Sören

      This functionality, which is the essence of generalized suffix tree:
      Given a set of multiple strings we would like to construct a single tree out of it.

      Where as Yona`s only create one tree for one string.
      For a more complete explanation on generalized suffix tree, please kindly refer to the link I gave in my OP.

Re: Generalized Suffix Tree in Perl
by tall_man (Parson) on Nov 23, 2005 at 14:37 UTC
Re: Generalized Suffix Tree in Perl
by Hanamaki (Chaplain) on Nov 24, 2005 at 09:26 UTC
    Or if you want to build your own routines, Rex A. Dwyer gives a gentle introduction on suffix trees in Chapter 12 (esp. pp. 177--193) of Genomic Perl using the word banana and not some DNA or RNA as one might fear.

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