Article View: bionet.molbio.evolution
Article #423Re: estimating branch length - phylip
From: Mary K. Kuhner
Date: Thu, 22 Feb 2007 20:33
Date: Thu, 22 Feb 2007 20:33
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In article <mailman.59.1172114161.5139.mol-evol@net.bio.net>, npriya <npriyarao@gmail.com> wrote: >I constructed a max likelihood tree (dnaml) after using seqboot (500 >bootstraps) and then performed a consense to get a final tree. The >tree looks fine but ofcourse it does not display branch lengths >(rather it displays bootstrap values). >So I took this tree, used retree to unroot and eliminate the bootstrap >values. I called this "intree". Now when I use the dnaml again with >the user tree option on the "intree" i am consistently getting an >error message which states that there is insufficient memory. I >understand that this problem is due to a badfile format but I don't >understand what could be wrong with my file. The user tree analysis needs both an intree and an infile containing the original sequence data. A very common error in Phylip is to have the wrong stuff in your infile--perhaps something left over from seqboot? The procedure you describe should work, so I suspect you have, as you say, a file problem--but I think it's likely in infile, not intree. Your tree looks okay to me. Mary Kuhner mkkuhner@u.washington.edu
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X-Google-Thread: 10a7a9,82ab29622a323570 X-Google-Attributes: gid10a7a9,public X-Google-Language: ENGLISH,ASCII-7-bit Path: arc1-ca.pugleaf.net!g2news2.google.com!news4.google.com!news.glorb.com!news.aset.psu.edu!news.cse.psu.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: estimating branch length - phylip Date: Thu, 22 Feb 2007 20:33:19 +0000 (UTC) Organization: Debian GNU/Linux site Lines: 26 Approved: BIOSCI Approval Key <biosci-approval-key@net.bio.net> Message-ID: <mailman.74.1172176513.5139.mol-evol@net.bio.net> References: <mailman.59.1172114161.5139.mol-evol@net.bio.net> NNTP-Posting-Host: kalo.bio.indiana.edu X-Trace: mailhub227.itcs.purdue.edu 1172176544 9494 129.79.224.26 (22 Feb 2007 20:35:44 GMT) X-Complaints-To: news@purdue.edu NNTP-Posting-Date: Thu, 22 Feb 2007 20:35:44 +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: 5.3.0.289146, Antispam-Engine: 2.5.0.283055, Antispam-Data: 2007.2.22.122434 X-Uwash-Spam: Gauge=IIIIIII, Probability=7%, Report='__C230066_P5 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, __SANE_MSGID 0' X-Mailman-Approved-At: Thu, 22 Feb 2007 15:35:12 -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 iQCVAwUBRd3+gqCIqsWvyF5FAQHGYwP/ZMoAwecr3Jq/Do9o++eBYu5GbzGA9UxG Qx49SGXXXee079EMxDIP8MGuY/f0P52L0TPkdpyZZRvyXNTNjN4+3mJ5RyyP85y+ OewhQ0+mIy/TxyKQEPQeHl+PcxalMhOnyerub+hkJ45hzvBXpj09+qG8kGt+l9gV ExbZ6lae7mw= =Eznr