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Article #2326Software to display genetic and geographical relationships - any suggestions?
From: Vince Mulholland
Date: Thu, 17 Sep 2009 09:13
Date: Thu, 17 Sep 2009 09:13
26 lines
3317 bytes
3317 bytes
Hi, I have some viral sequences from around the world. When I construct dendrograms they suggest a geographical relationship in the clustering of the sequences. Is there any software I can use which could simultaneously analyse genetic distances AND geographical distances to represent the clustering I can see. I had thought of principal co-ordinate analysis (PCA), but if there is something out there designed to do this sort of thing that would be better. Any suggestions (including how I could do a PCA on these data) would be gratefully received. Vince Vincent Mulholland Science and Advice for Scottish Agriculture (SASA) SASA is a Division of the Scottish Government Rural Payments and Inspections Directorate Correspondents should note that all communications to or from SASA (Science and Advice for Scottish Agriculture � a Division of the Rural Payments and Inspections Directorate of the Scottish Government) may be automatically logged, monitored and/or recorded for lawful purposes. The original of this email was scanned for viruses by the Government Secure Intranet (GSi) virus scanning service. On leaving the GSi this email was certified virus-free.
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X-Google-Thread: 6710630482,51fbe1966767b562,start X-Google-Attributes: gid6710630482,public,usenet X-Google-NewGroupId: yes X-Google-Language: ENGLISH,ASCII Path: arc1-ca.pugleaf.net!g2news2.google.com!news1.google.com!news.glorb.com!news.cse.ohio-state.edu!usenet01.sei.cmu.edu!elk.ncren.net!news.purdue.edu!not-for-mail From: "Vince Mulholland" <Vince.Mulholland@sasa.gsi.gov.uk> Newsgroups: bionet.software Subject: Software to display genetic and geographical relationships - any suggestions? Date: Thu, 17 Sep 2009 10:13:07 +0100 Organization: BIOSCI/IUBio, Biology Dept., Indiana University Lines: 27 Approved: BIOSCI Approval Key <biosci-approval-key@net.bio.net> Message-ID: <mailman.979.1253199890.21502.bio-soft@net.bio.net> NNTP-Posting-Host: kalo.bio.indiana.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-Trace: mailhub227.itcs.purdue.edu 1253199924 11409 129.79.224.26 (17 Sep 2009 15:05:24 GMT) X-Complaints-To: news@purdue.edu NNTP-Posting-Date: Thu, 17 Sep 2009 15:05:24 +0000 (UTC) To: <bio-soft@magpie.bio.indiana.edu> X-Envelope-From: Vince.Mulholland@sasa.gsi.gov.uk X-VirusChecked: Checked X-Env-Sender: Vince.Mulholland@sasa.gsi.gov.uk X-Msg-Ref: server-6.tower-185.messagelabs.com!1253178794!50285204!1 X-StarScan-Version: 6.1.3; banners=sasa.gsi.gov.uk,-,- X-Originating-IP: [62.25.106.208] content-class: urn:content-classes:message X-MimeOLE: Produced By Microsoft Exchange V6.0.6619.12 Thread-Topic: Software to display genetic and geographical relationships - any suggestions? Thread-Index: Aco3dxFjCEf4JyH+RJKKOw+n0rjMUQ== X-MIME-Autoconverted: from quoted-printable to 8bit by net.bio.net id n8H9DKp03096 X-Mailman-Approved-At: Thu, 17 Sep 2009 10:04:48 -0500 X-BeenThere: bio-soft@net.bio.net X-Mailman-Version: 2.1.4 Precedence: list X-Auth: PGPMoose V1.1 PGP bionet.software iQCVAwUBSrJQEqCIqsWvyF5FAQG55AP8DK9amePsUE8LoJHCVp+HGrMpQ5JAhR/N IeOx2Y4m+B5wu+E010Lcqw5wXnBG8klf/41p0S8uqazq4vp0YyDPFoI1qm+DLWyr SDTIghdnOAQKVITZtz6X/kiKr84cjD5CmqiDNtwI/TGDQ/l0983GKsxasbg042zW MV94PCPmmJM= =EYpo