syn-tax (best phenetics software thread) -Reply
DawsonM at LANDCARE.CRI.NZ
Tue Jul 15 16:58:00 CDT 1997
Three packages discussed in this thread, i.e., NTSYS-pc, SYN-TAX, and
PANKEY are all available from Exeter Software. The following site has
price and package details:
For more information on PANKEY see also:
>>> Tim Dickinson 9/July/1997 08:10am >>>
in reply to murray dawson's query re s/w for numerical phenetics, i
like to suggest checking out not only ntsys-pc and the delta add-ons, but
also the SYN-TAX pkg. available (like ntsys-pc) from exeter software (in
north america) or (elsewhere) from the author, janos podani:
podani at ludens.elte.hu or http://ramet.elte.hu/~podani (where you can
info re the book referred to below)
syn-tax has, imo, the following advantages:
(1) a wide range of resemblance coefficients are provided for use with
quantitative, qualitative, and mixed data. sufficient information is
supplied re each one that comparison with tables in legendre &
numerical taxonomy (or in subsequent article by gower & legendre; j.
classification 3(1):5-48, 1986) will allow the user to make intelligent
choices between them, based on data type, assumptions, and
(2) a wide range of well-documented hierarchical and non-hierarchical
clustering methods are laid on.
(3) ditto, ordination methods (including PCA, PCoA, canonical analyses,
correspondance analysis, etc.).
(4) classifications and ordinations can be compared algorithmically. a
little-known add-on permits the user to convert trees from nexus to
format, so that the multiple trees obtained in many cladistic analyes can
be compared efficiently (jp & tad, ca. j. bot. 62:2765-2778, 1984; cf. also
our poster at icseb-v, august 1996).
(5) descriptors can be ranked according to an assortment of criteria.
(6) the pkg. also provides routines for simulated sampling and analysis of
multi-species point patterns.
(7) podani has a useful book (1994) on multivariate analyses that is
on use of the syn-tax pkg.
(8) input consists of ascii text files (such as might be produced from a
DELTA database); output is similar, and graphics (dendrograms,
etc.) can be save as .pcx and .tif files. both mac and pc versions are
available, and the latter run under both windows 3.1 and 95 (as well as
dos); for both platforms there is a good, english-language user's
(9) in summary, if you want to be able to analyze your data thoroughly,
are prepared to learn something about the relevant methods at least at
level of padani's book, manly's book on m'variate statistical methods, or
legendre & legendre (op. cit.) then the syn-tax pkg. is well worth having.
for a recent example of use of syn-tax (as well as ntsys-pc and s-plus),
see tad & l. j. hutchison (mycol. res. 101(4): 477-492, 1997).
mac users might want to find out about pierre legendre's r package,
recently revised for power-pc machines, especially if you are interested
extensive analyses of spatial patterns, auto-correlation, etc. a possibly
out-of-date url for this pkg. is:
http://alize.ere.umontreal.ca/~casgrain/R-v3/ or you can try the following
address for philippe casgrain, casgrain at ere.umontreal.ca.
have fun with either of these! ---tad.
<Tim Dickinson (tim.dickinson at utoronto.ca, timd at rom.on.ca)
<Vascular Plant Herbarium (TRT)
<Center for Biodiversity and Conservation Biology
<Royal Ontario Museum
<100 Queen's Park
<Toronto ON Canada M5S 2C6
<Phone (416) 586 8032
<and other sites with links there
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