Article View: bionet.molbio.evolution
Article #470Re: Bootstrap interpretation
From: Mary K. Kuhner
Date: Tue, 10 Jun 2008 19:00
Date: Tue, 10 Jun 2008 19:00
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3808 bytes
In article <mailman.370.1213016647.3533.mol-evol@net.bio.net>, DimitryASuplatov <genesup@gmail.com> wrote: >I want to generate "random" alignment to use it as a neutral evolution >model for hypothesis testing. I need a phylogenetic tree of my species >for that. >I have used phylip package to generate a set of 1000 replicates, then I >have used PMB model to calculate the distances with protdist and finally >appllied neighbor and consese with default settings. >As a result a have an unrooted tree with bootstrap values generaly >better at the tips than in the center of the tree. In my understanding >this is a normal case, though some values are equal to 25%. >So my question is what could I do with this tree? As I understand, 25% >values emphasize the fact that different parts of distant sequnces do >not show consistency with overall comparison. I can not crop the >alignment. Should I use neighbor-joining to calculate the tree directly >from the alignment? >Thanks. I am having trouble understanding what you want to do here. Let me try to restate it. If I understand correctly, you would like to simulate random data on the same tree that generated your species. You are trying to get this by first making a bootstrap consensus tree of your species, and then (you don't describe this part) simulating data on that tree. This won't work, because the bootstrap consensus tree has no branch lengths, and you need branch lengths to simulate data. The usual approach is simply to infer the tree from your original data (by whatever method you prefer) and simulate data on that inferred tree. While the inferred tree will not be perfect, it should be generally similar to the unknown true tree and may be good enough for a neutrality test. If this is not what you are trying to do, could you restate it? Mary Kuhner mkkuhner@u.washington.edu
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X-Google-Thread: 10a7a9,963b0e6d6fde2c3c X-Google-Attributes: gid10a7a9,domainid0,public,usenet X-Google-Language: ENGLISH,ASCII-7-bit Path: arc1-ca.pugleaf.net!g2news1.google.com!news4.google.com!news3.google.com!news1.google.com!newsfeed.stanford.edu!elk.ncren.net!news.purdue.edu!not-for-mail From: mkkuhner@kingman.gs.washington.edu (Mary K. Kuhner) Newsgroups: bionet.molbio.evolution Subject: Re: Bootstrap interpretation Date: Tue, 10 Jun 2008 19:00:10 +0000 (UTC) Organization: Debian GNU/Linux site Lines: 43 Approved: BIOSCI Approval Key <biosci-approval-key@net.bio.net> Message-ID: <mailman.391.1213125777.3533.mol-evol@net.bio.net> References: <mailman.370.1213016647.3533.mol-evol@net.bio.net> NNTP-Posting-Host: kalo.bio.indiana.edu X-Trace: mailhub227.itcs.purdue.edu 1213125799 961 129.79.224.26 (10 Jun 2008 19:23:19 GMT) X-Complaints-To: news@purdue.edu NNTP-Posting-Date: Tue, 10 Jun 2008 19:23:19 +0000 (UTC) To: bionet-molbio-evolution@moderators.isc.org X-Envelope-From: news@u.washington.edu X-Newsreader: trn 4.0-test76 (Apr 2, 2001) Originator: mkkuhner@kingman.gs.washington.edu (Mary K. Kuhner) X-PMX-Version: 5.4.1.325704, Antispam-Engine: 2.6.0.325393, Antispam-Data: 2008.6.10.114447 X-Uwash-Spam: Gauge=IIIIIII, Probability=7%, Report='LEO_OBFU_SUBJ_RE 0.1, BODY_SIZE_1900_1999 0, BODY_SIZE_5000_LESS 0, __BOUNCE_CHALLENGE_SUBJ 0, __C230066_P5 0, __FRAUD_419_BODY_WEBMAIL 0, __FRAUD_419_WEBMAIL 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, __SANE_MSGID 0' X-Mailman-Approved-At: Tue, 10 Jun 2008 14:22:55 -0500 X-BeenThere: mol-evol@net.bio.net X-Mailman-Version: 2.1.4 Precedence: list X-Auth: PGPMoose V1.1 PGP bionet.molbio.evolution iQCVAwUBSE7UkqCIqsWvyF5FAQFmVAQAgLmdr0kNZwjUCagxPDtsM9JADC0d8oGv WyNnBffGjDfRZPAQBKGU01IFO5V9bEZ0pcjD6CJbJXwPmQBZkxfe0u1v+fD8vmgt jLq7mmu3Y4nuuvmxZiIZYmoeWjAuU3ci7rwUym0vmtidDlC6/bzCR7LAfidaAm8u VJ7A8pJXXEI= =VtZM