----- Forwarded message from andrea cardini <[email protected]> -----
Date: Wed, 13 Nov 2013 04:18:53 -0500
From: andrea cardini <[email protected]>
Reply-To: andrea cardini <[email protected]>
Subject: Re: UPGMA
To: [email protected]
Hi Giulia,
among the free programs, you can use PAST (menu
multivariate, cluster analysis, options
pair-group and Euclidean distances). You can use
either shape coordinates or all PCs of shape
coordinates that you can get from MorphoJ. Just
change "ID" (name of the first column) with
"label" or any other word which is not ID after
exporting the txt file from MorphoJ. Or, if you
have a TPS file, you can load it in PAST and do
the superimposition in PAST and then the UPGMA.
PAST does not project data in the tangent space,
I believe, but that generally does not make any
appreciable difference in shape distances and
thus phenograms (for most biological datasets, at least).
In PAST I would not use the bootstrap option when
one analyses Procrustes shape data (reasons
explained in Biological Journal of the Linnean
Society, 2008, 93, p. 829 available at:
https://sites.google.com/site/hymsfme/drandreacardini/publications ).
Good luck.
Cheers
Andrea
At 07:45 13/11/2013, you wrote:
>----- Forwarded message from Giulia Guidarelli
><[email protected]> -----
>
>Date: Sat, 9 Nov 2013 05:30:20 -0500
>From: Giulia Guidarelli <[email protected]>
>Reply-To: Giulia Guidarelli <[email protected]>
>Subject: UPGMA
>To: [email protected]
>
>Dear Sir,
>
>I would like to realize an UPGMA phenogram using
>the matrix of Procrustes distances.
>Which software should I use? Can I use MorphoJ?
>
>best regards,
>
>Giulia Guidarelli
>
><mailto:[email protected]>[email protected]
>
>
>
>----- End forwarded message -----
>
>
Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di
Scienze Chimiche e Geologiche, Università di
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy
Honorary Fellow, Centre for Anatomical and Human
Sciences, University of Hull, Cottingham Road,
Hull, HU6 7RX, UK & University of York, Heslington, York YO10 5DD, UK
Adjunct Associate Professor, Centre for Forensic
Science , The University of Western Australia, 35
Stirling Highway, Crawley WA 6009, Australia
E-mail address: [email protected], [email protected]
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at:
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html
FREE Yellow BOOK on Geometric Morphometrics:
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at:
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf
Editorial board for:
Zoomorphology:
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of
Mammalogy: http://www.italian-journal-of-mammalogy.it/
----- End forwarded message -----
