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DATE 2016-09-01 LEARN 2024-05-01 | 2024-04-01 | 2024-03-01 | 2024-02-01 | 2024-01-01 | 2023-12-01 | 2023-11-01 | 2023-10-01 | 2023-09-01 | 2023-08-01 | 2023-07-01 | 2023-06-01 | 2023-05-01 | 2023-04-01 | 2023-03-01 | 2023-02-01 | 2023-01-01 | 2022-12-01 | 2022-11-01 | 2022-10-01 | 2022-09-01 | 2022-08-01 | 2022-07-01 | 2022-06-01 | 2022-05-01 | 2022-04-01 | 2022-03-01 | 2022-02-01 | 2022-01-01 | 2021-12-01 | 2021-11-01 | 2021-10-01 | 2021-09-01 | 2021-08-01 | 2021-07-01 | 2021-06-01 | 2021-05-01 | 2021-04-01 | 2021-03-01 | 2021-02-01 | 2021-01-01 | 2020-12-01 | 2020-11-01 | 2020-10-01 | 2020-09-01 | 2020-08-01 | 2020-07-01 | 2020-06-01 | 2020-05-01 | 2020-04-01 | 2020-03-01 | 2020-02-01 | 2020-01-01 | 2019-12-01 | 2019-11-01 | 2019-10-01 | 2019-09-01 | 2019-08-01 | 2019-07-01 | 2019-06-01 | 2019-05-01 | 2019-04-01 | 2019-03-01 | 2019-02-01 | 2019-01-01 | 2018-12-01 | 2018-11-01 | 2018-10-01 | 2018-09-01 | 2018-08-01 | 2018-07-01 | 2018-06-01 | 2018-05-01 | 2018-04-01 | 2018-03-01 | 2018-02-01 | 2018-01-01 | 2017-12-01 | 2017-11-01 | 2017-10-01 | 2017-09-01 | 2017-08-01 | 2017-07-01 | 2017-06-01 | 2017-05-01 | 2017-04-01 | 2017-03-01 | 2017-02-01 | 2017-01-01 | 2016-12-01 | 2016-11-01 | 2016-10-01 | 2016-09-01 | 2016-08-01 | 2016-07-01 | 2016-06-01 | 2016-05-01 | 2016-04-01 | 2016-03-01 | 2016-02-01 | 2016-01-01 | 2015-12-01 | 2015-11-01 | 2015-10-01 | 2015-09-01 | 2015-08-01 | 2015-07-01 | 2015-06-01 | 2015-05-01 | 2015-04-01 | 2015-03-01 | 2015-02-01 | 2015-01-01 | 2014-12-01 | 2014-11-01 Key: Value: Key: Value: MESSAGE DATE 2016-09-25 FROM ruben safir SUBJECT Subject: [Learn] Fwd: Cladistics and Computational Math From learn-bounces-at-nylxs.com Sun Sep 25 03:05:42 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 337D5163E9A; Sun, 25 Sep 2016 03:05:42 -0400 (EDT) X-Original-To: learn-at-nylxs.com Delivered-To: learn-at-nylxs.com Received: from [10.0.0.62] (flatbush.mrbrklyn.com [10.0.0.62]) by mrbrklyn.com (Postfix) with ESMTP id 7F09A161469 for ; Sun, 25 Sep 2016 03:05:38 -0400 (EDT) References: To: learn-at-nylxs.com From: ruben safir X-Forwarded-Message-Id: Message-ID: <6ef2bb8e-4a5f-1415-ec31-dffac8f59804-at-mrbrklyn.com> Date: Sun, 25 Sep 2016 03:05:38 -0400 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Thunderbird/45.2.0 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/mixed; boundary="------------759B8E0163A4D92BBD5678BE" Subject: [Learn] Fwd: Cladistics and Computational Math 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: , Errors-To: learn-bounces-at-nylxs.com Sender: "Learn" This is a multi-part message in MIME format. --------------759B8E0163A4D92BBD5678BE Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit Please not this entire thread as it points us to where the paleontology field is currently holding with regard to the use of computers in producing cladistic trees. --------------759B8E0163A4D92BBD5678BE Content-Type: message/rfc822; name="Cladistics and Computational Math.eml" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Cladistics and Computational Math.eml" Path: reader2.panix.com!panix!not-for-mail From: Popping mad Newsgroups: sci.bio.paleontology Subject: Cladistics and Computational Math Date: Sat, 24 Sep 2016 13:37:19 +0000 (UTC) Organization: PANIX Public Access Internet and UNIX, NYC Message-ID: NNTP-Posting-Host: www.mrbrklyn.com Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Trace: reader2.panix.com 1474724239 2623 96.57.23.82 (24 Sep 2016 13:37:19 GMT) X-Complaints-To: abuse-at-panix.com NNTP-Posting-Date: Sat, 24 Sep 2016 13:37:19 +0000 (UTC) User-Agent: Pan/0.140 (Chocolate Salty Balls; GIT b8fc14e git.gnome.org/git/pan2) Xref: panix sci.bio.paleontology:67006 So, I've been given the go ahead to do my thesis on Machine Learning and Computational Mathematics in developing Cladistic Models of Evolution. I discussed here, previously, how map theory might be helpful in producing accurate interpretations of species relations. And it was told to me that such attempts have been made before and papers were notated in that discussion. Can someone give me, please, sources for previous work in this area and also a basic work on cladistics? Ruben http://www.nylxs.com/thesis/ --------------759B8E0163A4D92BBD5678BE Content-Type: message/rfc822; name="Re: Cladistics and Computational Math.eml" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Re: Cladistics and Computational Math.eml" Path: reader2.panix.com!panix!bloom-beacon.mit.edu!bloom-beacon.mit.edu!newsswitch.lcs.mit.edu!ottix-news.ottix.net!border1.nntp.dca1.giganews.com!nntp.giganews.com!buffer1.nntp.dca1.giganews.com!news.giganews.com.POSTED!not-for-mail NNTP-Posting-Date: Sat, 24 Sep 2016 08:46:09 -0500 Subject: Re: Cladistics and Computational Math Newsgroups: sci.bio.paleontology References: From: John Harshman Date: Sat, 24 Sep 2016 06:46:08 -0700 User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:45.0) Gecko/20100101 Thunderbird/45.3.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Message-ID: X-Usenet-Provider: http://www.giganews.com X-Trace: sv3-rnhsJ3C2/Fl5MGxVq3zgT6eEJE5yJHOPswHdUvbwxtsDH4glhOwOLrovyYsCIRWcvK/K4fjiV+i/rBD!/6lh3k073Nnu+aemElLmZCPSqy97TUujrkYLqxR7XRvaP+GDv/A68KTs/EVzzI39SLGJyW/+bbQ= X-Complaints-To: abuse-at-giganews.com X-DMCA-Notifications: http://www.giganews.com/info/dmca.html X-Abuse-and-DMCA-Info: Please be sure to forward a copy of ALL headers X-Abuse-and-DMCA-Info: Otherwise we will be unable to process your complaint properly X-Postfilter: 1.3.40 X-Original-Bytes: 2188 Xref: panix sci.bio.paleontology:67007 On 9/24/16 6:37 AM, Popping mad wrote: > So, I've been given the go ahead to do my thesis on Machine Learning and > Computational Mathematics in developing Cladistic Models of Evolution. I > discussed here, previously, how map theory might be helpful in producing > accurate interpretations of species relations. And it was told to me > that such attempts have been made before and papers were notated in that > discussion. Can someone give me, please, sources for previous work in > this area and also a basic work on cladistics? I don't know what map theory is, so can't point to any previous work. A basic work on cladistics, by which I assume you mean phylogenetics, is Inferring Phylogenies by Joe Felsenstein. (If you really do mean cladistics, which in this context is generally assumed to mean strict parsimony, that's in there too, but it's a small part.) You might want to look up some of the programs used for inference. Try searching on PHYLIP, PAUP, RaxML, GARLI, BEAST, MrBayes. --------------759B8E0163A4D92BBD5678BE Content-Type: message/rfc822; name="Re: Cladistics and Computational Math.eml" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Re: Cladistics and Computational Math.eml" Path: reader2.panix.com!panix!not-for-mail From: Popping mad Newsgroups: sci.bio.paleontology Subject: Re: Cladistics and Computational Math Date: Sat, 24 Sep 2016 17:48:46 +0000 (UTC) Organization: PANIX Public Access Internet and UNIX, NYC Message-ID: References: NNTP-Posting-Host: www.mrbrklyn.com Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Trace: reader2.panix.com 1474739326 5275 96.57.23.82 (24 Sep 2016 17:48:46 GMT) X-Complaints-To: abuse-at-panix.com NNTP-Posting-Date: Sat, 24 Sep 2016 17:48:46 +0000 (UTC) User-Agent: Pan/0.140 (Chocolate Salty Balls; GIT b8fc14e git.gnome.org/git/pan2) Xref: panix sci.bio.paleontology:67008 On Sat, 24 Sep 2016 06:46:08 -0700, John Harshman wrote: >> So, I've been given the go ahead to do my thesis on Machine Learning >> and Computational Mathematics in developing Cladistic Models of >> Evolution. I >> discussed here, previously, how map theory might be helpful in >> producing accurate interpretations of species relations. And it was >> told to me that such attempts have been made before and papers were >> notated in that discussion. Can someone give me, please, sources for >> previous work in this area and also a basic work on cladistics? > > I don't know what map theory is, so can't point to any previous work. We spent quite a bit of time discussing it and cladistics are a form of map theory so maybe you can clarify what you mean when you say that you don't know what map theory is. Maybe i would be clearer if I said Graph Theory similar to Dijkstra's algorithm? > A > basic work on cladistics, by which I assume you mean phylogenetics, is > Inferring Phylogenies by Joe Felsenstein. (If you really do mean > cladistics, which in this context is generally assumed to mean strict > parsimony, that's in there too, but it's a small part.) > I'd dealing with the morphology of fossils only. So that would not be cladistics? > You might want to look up some of the programs used for inference. Try > searching on PHYLIP, PAUP, RaxML, GARLI, BEAST, MrBayes. Thank You! --------------759B8E0163A4D92BBD5678BE Content-Type: message/rfc822; name="Re: Cladistics and Computational Math.eml" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Re: Cladistics and Computational Math.eml" Path: reader2.panix.com!panix!goblin2!goblin1!goblin.stu.neva.ru!eternal-september.org!feeder.eternal-september.org!news.eternal-september.org!.POSTED!not-for-mail From: RSNorman Newsgroups: sci.bio.paleontology Subject: Re: Cladistics and Computational Math Date: Sat, 24 Sep 2016 14:19:49 -0400 Organization: A noiseless patient Spider Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Injection-Info: mx02.eternal-september.org; posting-host="8658724397e90fde6dd30473cef11e2a"; logging-data="32076"; mail-complaints-to="abuse-at-eternal-september.org"; posting-account="U2FsdGVkX18vFhznJk2jABn2cXAv1AtaiXyfSrb00dU=" X-Newsreader: Forte Agent 6.00/32.1186 Cancel-Lock: sha1:TV7SzSL1ZqtRtK90wYxXg3TRLS0= Xref: panix sci.bio.paleontology:67009 On Sat, 24 Sep 2016 17:48:46 +0000 (UTC), Popping mad wrote: >On Sat, 24 Sep 2016 06:46:08 -0700, John Harshman wrote: > >>> So, I've been given the go ahead to do my thesis on Machine Learning >>> and Computational Mathematics in developing Cladistic Models of >>> Evolution. I >>> discussed here, previously, how map theory might be helpful in >>> producing accurate interpretations of species relations. And it was >>> told to me that such attempts have been made before and papers were >>> notated in that discussion. Can someone give me, please, sources for >>> previous work in this area and also a basic work on cladistics? >> >> I don't know what map theory is, so can't point to any previous work. > >We spent quite a bit of time discussing it and cladistics are a form of >map theory so maybe you can clarify what you mean when you say that you >don't know what map theory is. > >Maybe i would be clearer if I said Graph Theory similar to Dijkstra's >algorithm? > > You are a computer scientist talking with a biologist. You come from different backgrounds and assume rather different levels of assumed knowledge in different subjects. Just because biologists talk about trees doesn't mean that biologists are up on graph theory and data structures. --------------759B8E0163A4D92BBD5678BE Content-Type: message/rfc822; name="Re: Cladistics and Computational Math.eml" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Re: Cladistics and Computational Math.eml" Path: reader2.panix.com!panix!usenet.stanford.edu!news.glorb.com!peer01.iad!feed-me.highwinds-media.com!news.highwinds-media.com!border1.nntp.dca1.giganews.com!nntp.giganews.com!buffer1.nntp.dca1.giganews.com!news.giganews.com.POSTED!not-for-mail NNTP-Posting-Date: Sat, 24 Sep 2016 14:41:20 -0500 Subject: Re: Cladistics and Computational Math Newsgroups: sci.bio.paleontology References: From: John Harshman Date: Sat, 24 Sep 2016 12:41:20 -0700 User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:45.0) Gecko/20100101 Thunderbird/45.3.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit Message-ID: X-Usenet-Provider: http://www.giganews.com X-Trace: sv3-9LBro2DqULAGkdnyg3tVf358fCRWUg4afCiymXH0IPIwQbLbr7M51ifEj1sk/ZTeXkc/waKn7HfMCDG!uskFV8GLHnbosDcN6j6YSFfbCep8eow/t3mooW/Q5gpaTyB6nEstWbcfpyiHbjQHoh6K26/zoBiD X-Complaints-To: abuse-at-giganews.com X-DMCA-Notifications: http://www.giganews.com/info/dmca.html X-Abuse-and-DMCA-Info: Please be sure to forward a copy of ALL headers X-Abuse-and-DMCA-Info: Otherwise we will be unable to process your complaint properly X-Postfilter: 1.3.40 X-Original-Bytes: 2838 X-Received-Bytes: 2929 X-Received-Body-CRC: 3946578297 Xref: panix sci.bio.paleontology:67011 On 9/24/16 11:19 AM, RSNorman wrote: > On Sat, 24 Sep 2016 17:48:46 +0000 (UTC), Popping mad > wrote: > >> On Sat, 24 Sep 2016 06:46:08 -0700, John Harshman wrote: >> >>>> So, I've been given the go ahead to do my thesis on Machine Learning >>>> and Computational Mathematics in developing Cladistic Models of >>>> Evolution. I >>>> discussed here, previously, how map theory might be helpful in >>>> producing accurate interpretations of species relations. And it was >>>> told to me that such attempts have been made before and papers were >>>> notated in that discussion. Can someone give me, please, sources for >>>> previous work in this area and also a basic work on cladistics? >>> >>> I don't know what map theory is, so can't point to any previous work. >> >> We spent quite a bit of time discussing it and cladistics are a form of >> map theory so maybe you can clarify what you mean when you say that you >> don't know what map theory is. >> >> Maybe i would be clearer if I said Graph Theory similar to Dijkstra's >> algorithm? >> >> > > You are a computer scientist talking with a biologist. You come from > different backgrounds and assume rather different levels of assumed > knowledge in different subjects. > > Just because biologists talk about trees doesn't mean that biologists > are up on graph theory and data structures. Well, I'm up a little on data structures. Data structures are generally the way trees are represented in programs. --------------759B8E0163A4D92BBD5678BE Content-Type: message/rfc822; name="Re: Cladistics and Computational Math.eml" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Re: Cladistics and Computational Math.eml" Path: reader2.panix.com!panix!usenet.stanford.edu!news.glorb.com!peer02.iad!feed-me.highwinds-media.com!news.highwinds-media.com!border1.nntp.dca1.giganews.com!nntp.giganews.com!buffer1.nntp.dca1.giganews.com!buffer2.nntp.dca1.giganews.com!news.giganews.com.POSTED!not-for-mail NNTP-Posting-Date: Sat, 24 Sep 2016 14:40:30 -0500 Subject: Re: Cladistics and Computational Math Newsgroups: sci.bio.paleontology References: From: John Harshman Date: Sat, 24 Sep 2016 12:40:30 -0700 User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:45.0) Gecko/20100101 Thunderbird/45.3.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Message-ID: X-Usenet-Provider: http://www.giganews.com X-Trace: sv3-1dwMvDlRITaclSKlPFuxRBdlnsebuevsAfEQlchADPce7Yvtq0AW99msXTUwax8t9Uf+1HtGtIVXdf/!IsvmCQyZ2HOvdfsY7vYIY2qtOy1RZuIrKyashR1BuZN4miNa6mOY/zf5jvYixmEov57uruoyXIcn X-Complaints-To: abuse-at-giganews.com X-DMCA-Notifications: http://www.giganews.com/info/dmca.html X-Abuse-and-DMCA-Info: Please be sure to forward a copy of ALL headers X-Abuse-and-DMCA-Info: Otherwise we will be unable to process your complaint properly X-Postfilter: 1.3.40 X-Original-Bytes: 3153 X-Received-Bytes: 3275 X-Received-Body-CRC: 1113983861 Xref: panix sci.bio.paleontology:67010 On 9/24/16 10:48 AM, Popping mad wrote: > On Sat, 24 Sep 2016 06:46:08 -0700, John Harshman wrote: > >>> So, I've been given the go ahead to do my thesis on Machine Learning >>> and Computational Mathematics in developing Cladistic Models of >>> Evolution. I >>> discussed here, previously, how map theory might be helpful in >>> producing accurate interpretations of species relations. And it was >>> told to me that such attempts have been made before and papers were >>> notated in that discussion. Can someone give me, please, sources for >>> previous work in this area and also a basic work on cladistics? >> >> I don't know what map theory is, so can't point to any previous work. > > We spent quite a bit of time discussing it and cladistics are a form of > map theory so maybe you can clarify what you mean when you say that you > don't know what map theory is. > > Maybe i would be clearer if I said Graph Theory similar to Dijkstra's > algorithm? No. All I know is how phylogenetics works, not what sort of mathematics you would like to use on it. If that's map theory or graph theory, fine, but not a concern of mine. >> A >> basic work on cladistics, by which I assume you mean phylogenetics, is >> Inferring Phylogenies by Joe Felsenstein. (If you really do mean >> cladistics, which in this context is generally assumed to mean strict >> parsimony, that's in there too, but it's a small part.) > > I'd dealing with the morphology of fossils only. So that would not be > cladistics? Depends on what you mean by cladistics. What do you mean? There are methods used for morphological phylogeny that do not rely on strict parsimony, though parsimony is still probably the most common. >> You might want to look up some of the programs used for inference. Try >> searching on PHYLIP, PAUP, RaxML, GARLI, BEAST, MrBayes. > > Thank You! > --------------759B8E0163A4D92BBD5678BE Content-Type: message/rfc822; name="Re: Cladistics and Computational Math.eml" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Re: Cladistics and Computational Math.eml" Path: reader2.panix.com!panix!not-for-mail From: ruben safir Newsgroups: sci.bio.paleontology Subject: Re: Cladistics and Computational Math Date: Sat, 24 Sep 2016 17:21:08 -0400 Organization: PANIX Public Access Internet and UNIX, NYC Message-ID: References: NNTP-Posting-Host: www.mrbrklyn.com Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit X-Trace: reader2.panix.com 1474752069 22474 96.57.23.82 (24 Sep 2016 21:21:09 GMT) X-Complaints-To: abuse-at-panix.com NNTP-Posting-Date: Sat, 24 Sep 2016 21:21:09 +0000 (UTC) User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Thunderbird/45.2.0 In-Reply-To: Xref: panix sci.bio.paleontology:67012 On 09/24/2016 03:40 PM, John Harshman wrote: > > Depends on what you mean by cladistics. What do you mean? There are > methods used for morphological phylogeny that do not rely on strict > parsimony, though parsimony is still probably the most common. What is the definition of the word parsimony in regards to evolutionary biology. It can't be the economics term I'm used to. --------------759B8E0163A4D92BBD5678BE Content-Type: message/rfc822; name="Re: Cladistics and Computational Math.eml" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Re: Cladistics and Computational Math.eml" Path: reader2.panix.com!panix!bloom-beacon.mit.edu!bloom-beacon.mit.edu!newsswitch.lcs.mit.edu!ottix-news.ottix.net!border1.nntp.dca1.giganews.com!nntp.giganews.com!buffer1.nntp.dca1.giganews.com!news.giganews.com.POSTED!not-for-mail NNTP-Posting-Date: Sat, 24 Sep 2016 18:12:09 -0500 Subject: Re: Cladistics and Computational Math Newsgroups: sci.bio.paleontology References: From: John Harshman Date: Sat, 24 Sep 2016 16:12:09 -0700 User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:45.0) Gecko/20100101 Thunderbird/45.3.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Message-ID: X-Usenet-Provider: http://www.giganews.com X-Trace: sv3-FLXWPZ0TxiynnPt311wet+WDcNv6+u1sS9XwzpCAXnbk/n/Nbg7v8mcx7zqs9ZDxOtINoxYtmsra9zK!EVVeLmGdk+2/xymU+6vBaJvj4CituAzcASXfw/CDKs9Axeji+5JOpp6Iia4FfVlfkLohRTwIClU= X-Complaints-To: abuse-at-giganews.com X-DMCA-Notifications: http://www.giganews.com/info/dmca.html X-Abuse-and-DMCA-Info: Please be sure to forward a copy of ALL headers X-Abuse-and-DMCA-Info: Otherwise we will be unable to process your complaint properly X-Postfilter: 1.3.40 X-Original-Bytes: 2713 Xref: panix sci.bio.paleontology:67013 On 9/24/16 2:21 PM, ruben safir wrote: > On 09/24/2016 03:40 PM, John Harshman wrote: >> >> Depends on what you mean by cladistics. What do you mean? There are >> methods used for morphological phylogeny that do not rely on strict >> parsimony, though parsimony is still probably the most common. > > What is the definition of the word parsimony in regards to evolutionary > biology. It can't be the economics term I'm used to. > These are the buzzwords you have to learn if you want to deal with phylogenetics. Here's a short primer, beginning with a detour. Phylogenetic analyses act on data sets to produce favored trees. Most methods do this by first setting a numerical optimality criterion, assessing that criterion for lots and lots of candidate trees, and picking the one that's best by that criterion. Parsimony is one such criterion. Briefly, a tree's parsimony score is the minimum number of character state changes, somewhere on the tree, necessary to explain the distribution of all character states in the terminal taxa. Parsimony algorithms perform the calculations necessary to determine the parsimony score. The lower the score, that is, the fewer the required changes, the better. (Let's leave aside the historical reasons for the name "parsimony". It has to do with philosophy of science, specifically Karl Popper.) --------------759B8E0163A4D92BBD5678BE Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Learn mailing list Learn-at-nylxs.com http://lists.mrbrklyn.com/mailman/listinfo/learn --------------759B8E0163A4D92BBD5678BE-- 2016-09-01 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: LIU CS course 2016-09-04 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] LIU Brooklyn Student Update 2016-09-04 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] LIU Brooklyn Student Update 2016-09-04 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Lockout 2016-09-08 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Computer Sciences 2016-09-10 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] LIU Lock Out 2016-09-10 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] [Hangout-NYLXS] Fwd: LIU Lock Out 2016-09-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Lock Out 2016-09-12 Amy Rothenberg <Amy.Rothenberg-at-liu.edu> Re: [Learn] LIU Lock Out 2016-09-13 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [isoc-ny] ISOC-NY joins coalition of groups supporting 2016-09-14 From: "Ruben.Safir" <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: Calendar Update 2016-09-19 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: Thesis option 2016-09-21 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fossil computational oppurtunities 2016-09-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fossil computational oppurtunities 2016-09-22 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] Sad News 2016-09-23 Christopher League <league-at-contrapunctus.net> Re: [Learn] Thesis - topic Machine learning in the determination of 2016-09-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Thesis - topic Machine learning in the determination of the 2016-09-25 ruben safir <ruben-at-mrbrklyn.com> Re: [Learn] Cladistics and Computational Math 2016-09-25 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Thesis 2016-09-25 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Thesis - topic Machine learning in the determination of 2016-09-25 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Cladistics and Computational Math 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Proposed Thesis 2016-09-26 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] Proposed Thesis 2016-09-26 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] Proposed Thesis 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Proposed Thesis 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Proposed Thesis 2016-09-27 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] phylip 2016-09-27 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] phylip 2016-09-27 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] t-rex web server 2016-09-28 From: "Pinsdorf, Michelle" <PinsdorfM-at-si.edu> Re: [Learn] little can be better 2016-09-28 From: "Pinsdorf, Michelle" <PinsdorfM-at-si.edu> Re: [Learn] little can be better 2016-09-28 league-at-contrapunctus.net Re: [Learn] meet up for thesis? 2016-09-28 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] meet up for thesis? 2016-09-28 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] meet up for thesis? 2016-09-28 Maneesh Kongara <maneeshkongara-at-gmail.com> Re: [Learn] meet up for thesis? 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] meet up for thesis? 2016-09-28 Christopher League <league-at-contrapunctus.net> Re: [Learn] Thesis - topic Machine learning in the determination of 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] meet up for thesis? 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Notice: Learn Mailing List for LIU 2016-09-28 Ben Creisler <bcreisler-at-gmail.com> Subject: [Learn] [dinosaur] T. rex tail CT scan + Utahraptor quicksand death 2016-09-28 Ben Creisler <bcreisler-at-gmail.com> Subject: [Learn] [dinosaur] T. rex tail CT scan + Utahraptor quicksand death 2016-09-29 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] Announcing LIU Votes 2016! 2016-09-29 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] phylogenetics 2016-09-29 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] phylogenetics 2016-09-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] two textbooks 2016-09-30 league-at-contrapunctus.net Re: [Learn] Thesis data 2016-09-30 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Thesis data 2016-09-30 league-at-contrapunctus.net Re: [Learn] Thesis data 2016-09-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Thesis data NYLXS are Do'ers and the first step of Doing is Joining! 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