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DATE 2016-11-01 LEARN 2024-11-21 | 2024-10-21 | 2024-09-21 | 2024-08-21 | 2024-07-21 | 2024-06-21 | 2024-05-21 | 2024-04-21 | 2024-03-21 | 2024-02-21 | 2024-01-21 | 2023-12-21 | 2023-11-21 | 2023-10-21 | 2023-09-21 | 2023-08-21 | 2023-07-21 | 2023-06-21 | 2023-05-21 | 2023-04-21 | 2023-03-21 | 2023-02-21 | 2023-01-21 | 2022-12-21 | 2022-11-21 | 2022-10-21 | 2022-09-21 | 2022-08-21 | 2022-07-21 | 2022-06-21 | 2022-05-21 | 2022-04-21 | 2022-03-21 | 2022-02-21 | 2022-01-21 | 2021-12-21 | 2021-11-21 | 2021-10-21 | 2021-09-21 | 2021-08-21 | 2021-07-21 | 2021-06-21 | 2021-05-21 | 2021-04-21 | 2021-03-21 | 2021-02-21 | 2021-01-21 | 2020-12-21 | 2020-11-21 | 2020-10-21 | 2020-09-21 | 2020-08-21 | 2020-07-21 | 2020-06-21 | 2020-05-21 | 2020-04-21 | 2020-03-21 | 2020-02-21 | 2020-01-21 | 2019-12-21 | 2019-11-21 | 2019-10-21 | 2019-09-21 | 2019-08-21 | 2019-07-21 | 2019-06-21 | 2019-05-21 | 2019-04-21 | 2019-03-21 | 2019-02-21 | 2019-01-21 | 2018-12-21 | 2018-11-21 | 2018-10-21 | 2018-09-21 | 2018-08-21 | 2018-07-21 | 2018-06-21 | 2018-05-21 | 2018-04-21 | 2018-03-21 | 2018-02-21 | 2018-01-21 | 2017-12-21 | 2017-11-21 | 2017-10-21 | 2017-09-21 | 2017-08-21 | 2017-07-21 | 2017-06-21 | 2017-05-21 | 2017-04-21 | 2017-03-21 | 2017-02-21 | 2017-01-21 | 2016-12-21 | 2016-11-21 | 2016-10-21 | 2016-09-21 | 2016-08-21 | 2016-07-21 | 2016-06-21 | 2016-05-21 | 2016-04-21 | 2016-03-21 | 2016-02-21 | 2016-01-21 | 2015-12-21 | 2015-11-21 | 2015-10-21 | 2015-09-21 | 2015-08-21 | 2015-07-21 | 2015-06-21 | 2015-05-21 | 2015-04-21 | 2015-03-21 | 2015-02-21 | 2015-01-21 | 2014-12-21 | 2014-11-21 | 2014-10-21 Key: Value: Key: Value: MESSAGE DATE 2016-11-02 FROM Ruben Safir SUBJECT Subject: [Learn] Fitch Algorithm - C++ From learn-bounces-at-nylxs.com Wed Nov 2 14:27:54 2016 Return-Path: X-Original-To: archive-at-mrbrklyn.com Delivered-To: archive-at-mrbrklyn.com Received: from www.mrbrklyn.com (www.mrbrklyn.com [96.57.23.82]) by mrbrklyn.com (Postfix) with ESMTP id E0BC1161312; Wed, 2 Nov 2016 14:27:53 -0400 (EDT) X-Original-To: learn-at-nylxs.com Delivered-To: learn-at-nylxs.com Received: by mrbrklyn.com (Postfix, from userid 1000) id 74F31161311; Wed, 2 Nov 2016 14:27:51 -0400 (EDT) Date: Wed, 2 Nov 2016 14:27:51 -0400 From: Ruben Safir To: learn-at-nylxs.com Message-ID: <20161102182751.GA10998-at-www.mrbrklyn.com> MIME-Version: 1.0 Content-Disposition: inline User-Agent: Mutt/1.5.21 (2010-09-15) Subject: [Learn] Fitch Algorithm - C++ X-BeenThere: learn-at-nylxs.com X-Mailman-Version: 2.1.17 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Errors-To: learn-bounces-at-nylxs.com Sender: "Learn" I started outlining and working on the Fitch algorithm as it is laid out in the text. I have some doubts about our understanding of the algorithm, but regardless, I've started working on it. I decided, FWIW, to do this in C++, just because I've forgotten how to do write C++ code and need to bring myself up to speed. Also, the nodal nature of this methodology lends itself to templates and classes. I'm looking at the general data structure of the method and this is what I've come up with. Critcism is welcome. Class Node Node parent Node lchild Node rchild vector <> int min Class State String name Class Costs State alpha State beta int cost vetcor<> I have C++ workshops with source at http://www.nylxs.com/workshop/ -- So many immigrant groups have swept through our town that Brooklyn, like Atlantis, reaches mythological proportions in the mind of the world - RI Safir 1998 http://www.mrbrklyn.com DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002 http://www.nylxs.com - Leadership Development in Free Software http://www2.mrbrklyn.com/resources - Unpublished Archive http://www.coinhangout.com - coins! http://www.brooklyn-living.com Being so tracked is for FARM ANIMALS and and extermination camps, but incompatible with living as a free human being. -RI Safir 2013 _______________________________________________ Learn mailing list Learn-at-nylxs.com http://lists.mrbrklyn.com/mailman/listinfo/learn 2016-11-01 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] how is it indexing in cuda 2016-11-01 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] not adequately speced of explained 2016-11-01 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] how is it indexing in cuda 2016-11-01 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] not adequately speced of explained 2016-11-02 Christopher League <league-at-contrapunctus.net> Re: [Learn] Fitch Algorithm - C++ 2016-11-02 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fitch Algorithm - C++ 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] how is it indexing in cuda 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fitch Algorithm - C++ 2016-11-02 IEEE Computer Society <csconnection-at-computer.org> Subject: [Learn] Hear Google's John Martinis Take on Quantum Computing at 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] opencl 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] scheduled for tommorw 2016-11-02 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] threads tutorial 2016-11-03 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fitch Algorithm - C++ 2016-11-03 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fitch Algorithm - C++ 2016-11-03 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fitch Algorithm - C++ 2016-11-03 Christopher League <league-at-contrapunctus.net> Re: [Learn] huffman code 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] huffman code 2016-11-03 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] huffman code 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fitch algorithm from the beginning 2016-11-03 From: <mrbrklyn-at-panix.com> Subject: [Learn] huffman code 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Phenology meeting 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] relevant hackathon 2016-11-03 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] relevant hackathon 2016-11-04 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] huffman code 2016-11-04 Christopher League <league-at-contrapunctus.net> Subject: [Learn] Fitch/Sankoff 2016-11-05 Christopher League <league-at-contrapunctus.net> Re: [Learn] Fwd: templates within templates 2016-11-05 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: const T vs T const 2016-11-05 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Template Library files and Header linking troubles 2016-11-05 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: templates within templates 2016-11-06 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fwd: templates within templates 2016-11-06 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: templates within templates 2016-11-06 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fwd: templates within templates 2016-11-06 Christopher League <league-at-contrapunctus.net> Re: [Learn] Fwd: templates within templates 2016-11-06 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Fwd: templates within templates 2016-11-06 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: templates within templates 2016-11-06 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: templates within templates 2016-11-06 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] GNU Parallel 20161022 ('Matthew') released [stable] 2016-11-07 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] templates and ostream for future reference 2016-11-08 Christopher League <league-at-contrapunctus.net> Re: [Learn] C++ signature ambiguity 2016-11-08 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] C++ signature ambiguity 2016-11-08 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] C++ signature ambiguity 2016-11-08 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Invitation: Phylogeny meeting -at- Weekly from 10:15 to 2016-11-08 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] Fwd: [nylug-talk] RSVP open: Wed Nov 16, 2016-11-09 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort parallel hw 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] merge sort parallel hw 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] merge sort parallel hw 2016-11-09 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort parallel hw 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] mergesort tutorial 2016-11-09 Christopher League <league-at-contrapunctus.net> Re: [Learn] mergesort tutorial 2016-11-09 Christopher League <league-at-contrapunctus.net> Re: [Learn] namespace and external files confusion 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] namespace and external files confusion 2016-11-09 From: "Carlos R. Mafra" <crmafra-at-gmail.com> Re: [Learn] Question about a small change 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] =?utf-8?q?C++_call_of_overloaded_=E2=80=98track=28int*=26?= 2016-11-09 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: lost arguments 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [dinosaur] Dating origins of dinosaurs, 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] merge sort parallel hw 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] mergesort tutorial 2016-11-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] namespace and external files confusion 2016-11-10 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort parallel hw 2016-11-10 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] merge sort parallel hw 2016-11-10 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] merge sort parallel hw 2016-11-10 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] merge sort parallel hw 2016-11-10 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] [Hangout-NYLXS] mergesort tutorial 2016-11-10 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] Fwd: [Hangout-NYLXS] ease your mind- everything in the 2016-11-10 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: [Hangout-NYLXS] R Programming Workshop 2016-11-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Paleocast phenogenetic tree building 2016-11-11 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort parallel hw 2016-11-12 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] HW of mergesort in parallel 2016-11-13 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] merge sort in parallel assignment 2016-11-14 Christopher League <league-at-contrapunctus.net> Re: [Learn] merge sort in parallel assignment 2016-11-14 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] merge sort in parallel assignment 2016-11-14 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] merge sort parallel hw 2016-11-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] CUDA and video 2016-11-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] PNG Graphic formats and CRCs 2016-11-15 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: PNG coding 2016-11-15 ruben safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: PNG Coding 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: lost arguments 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] relevant hackathon 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] C++ Workshop Announcement 2016-11-16 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] Fwd: Re: ref use 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] ref use 2016-11-16 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] why use a reference wrapper int his example 2016-11-17 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] [Hangout-NYLXS] at K&R now 2016-11-17 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [Hangout-NYLXS] Fwd: PNG Coding 2016-11-18 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] C++ workshop and usenet responses 2016-11-19 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: ref use 2016-11-20 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] when is the constructor called for an object 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: creating a binary tree 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: hidden static 2016-11-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: ISBI 2017 Call for Abstracts and Non-Author 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: PNG coding 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: the new {} syntax 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: when is the constructor called for an object 2016-11-21 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: when is the constructor called for an object 2016-11-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [dinosaur] Eoconfuciusornis feather keratin and 2016-11-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] look what I found 2016-11-22 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Cuccuency book 2016-11-22 ruben safir <ruben.safir-at-my.liu.edu> Subject: [Learn] declare a func or call an object 2016-11-22 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: Re: Using CLIPS as a library 2016-11-23 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: Simple C++11 Wrapper for CLIPS 6.30 2016-11-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Parrelel Programming HW2 with maxpath 2016-11-24 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] great research news for big data 2016-11-24 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] mapping algorithms 2016-11-24 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Todays meeting 2016-11-25 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [dinosaur] Flightless theropod phylogenetic variation 2016-11-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Note to self for Thursday 2016-11-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fitch etc 2016-11-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Note to self for Thursday 2016-11-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] operator<<() overloading details and friend 2016-11-27 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] 130 year old feathers analysis 2016-11-27 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: ACM/SPEC ICPE 2017 - Call for Tutorial Proposals 2016-11-27 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: ACM/SPEC ICPE 2017 - Call for Workshop Proposals 2016-11-27 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: CfP 22nd Conf. Reliable Software Technologies, 2016-11-27 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Seeking contributors for psyche-c 2016-11-29 Christopher League <league-at-contrapunctus.net> Re: [Learn] Look at this exciting output by my test program 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Look at this exciting output by my test program 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Look at this exciting output by my test program 2016-11-29 Christopher League <league-at-contrapunctus.net> Re: [Learn] Quantum Entanglement 2016-11-29 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Quantum Entanglement 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Here is the paper I was talking out 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Look at this exciting output by my test program 2016-11-29 nylxs <mrbrklyn-at-optonline.net> Subject: [Learn] Look at this exciting output by my test program 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Quantum Entanglement 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] The Death of PBS 2016-11-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] witmer lab ohio and 3d imaging 2016-11-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] phylogenetic crawler NYLXS are Do'ers and the first step of Doing is Joining! 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