[Taxacom] software recommendation please

Mathias Tobler mtlist at gmx.net
Mon Nov 19 15:14:29 CST 2007


Two software packages that do all multivariate analysis and are free are

Ginkgo
http://biodiver.bio.ub.es/vegana/
http://aefa.unileon.es/PDF/Font/GINKGO-JVS1.pdf

and the BiodiversityR package for R
http://cran.nedmirror.nl/src/contrib/Descriptions/BiodiversityR.html
http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp

Both were designed for vegetation analsysis but do all sorts of 
multivariate analysis including clustering and nometric 
multidimensional scaling (NMDS) on a variety of similarity 
measurements. Ginkgo is easier to use unless you are already familiar 
with R. Both run under the most common operating systems.

Mathias





At 10:26 13.11.2007, Soowon Cho wrote:
>Dear members,
>
>A friend of mine asked me about how to group his microorgarnisms based on
>certain reactions among each others, but I am not familiar with such.  He
>said his data is like the following:
>     A   B   C   D  .....
>A  0   1    0    1
>B  1   0    0    0
>C  0   1    0    1
>D  1   0    0    0
>:
>
>For the above, A is responding to B and D only, B is responding to A only, C
>is responding to B and D only,.....etc.
>His data is with nearly a hundred OTUs and he wants to know which software
>is good to use for grouping them based on the result.
>
>My initial thought was about UPGMA or PCA, but I am not sure.  Could anyone
>tell me which method (software) is good to analyze this kind of data for
>grouping based on "similarity"(I guess)?
>
>Sincerely,
>_______________________________________________
>Taxacom mailing list
>Taxacom at mailman.nhm.ku.edu
>http://mailman.nhm.ku.edu/mailman/listinfo/taxacom





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