syn-tax (best phenetics software thread)

[Tim Dickinson]

in reply to murray dawson's query re s/w for numerical phenetics, i would
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 find
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 & legendre's
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 objectives.

(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 syn-tax
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 based
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, ordinations,
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
manual.

(9) in summary, if you want to be able to analyze your data thoroughly, and
are prepared to learn something about the relevant methods at least at the
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 in
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
<
<see also:
<http://www.botany.utoronto.ca/faculty/dickinson/t_dickinson.html
<and other sites with links there
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