---+ Broken Telephone Tree <blockquote> _You are the director of a secret police agency, pitted against an imaginary organization using the nefarious tactic of a phone tree. You decide how much information to share with other secret police agencies in reconstructing the structure of the network..._ </blockquote> Message analysis from a telephone tree with noise (in the form of edit-distance paths between dictionary words). Equivalent to certain problems in molecular evolution & phylogenetic reconstruction. <!-- * [[BiowikiCvsCheckout:reader-bioe131/wordmatch/sheet.pdf][Fall 2008 handout]] for Teaching.BioE131 (64-page PDF, double-sided) * [[Fall08.TreeThing][Fall 2008 student page]] with 32 sentences summarized --> Background: * Wikipedia:Telephone_game * Examples of a "telephone tree": * [[http://www.wisegeek.com/what-is-a-phone-tree.htm]["What is a phone tree?"]] -- article @wisegeek.com * http://www.ehow.com/how_4325_set-emergency-phone.html * http://www.aauw.org/advocacy/issue_advocacy/phonetree.cfm * http://www.state.nj.us/military//familysupport/family_readiness/telephone_tree.html Some more links: * [[Edit distance]] * UPGMA algorithm for phylogenetic reconstruction * [[Distance matrix]] format * Other bioinformatics pseudo-[[cryptanalysis exercises]] <blockquote> *<nop>BioE131/231:* If you have done the following labs, then you have the tools to solve this problem (and obtain extra credit): * SequenceAlignmentLab * PrimatePhylogeny And if you have done the following homeworks, then you have *built your own versions* of the tools you need to solve this problem: * PairwiseAlignmentHomework * PhylogenyHomework </blockquote> ---+ Source code * [[BiowikiCvsCheckout:reader-bioe131/wordmatch/evolve.cc][C++ source code]] <small>([[BiowikiCvsCheckout:reader-bioe131/wordmatch/sheet.tex][LaTeX]]; [[BiowikiCvsCheckout:reader-bioe131/wordmatch/Makefile][Makefile]])</small> -- Main.IanHolmes - 26 Nov 2008
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