Dear all,
I have a set of SSR data from individual trees belonging to diferent walnut species so I would like to construct a dendrogram with this data but I can't find a suitable software to do this. Some year ago I have used PowerMarker but now it's not available. Could you advise me about it?
Thanks
Hello, I recommend InfoStat, which comes with an interface to connect directly with R. http://www.infostat.com.ar/index.php?mod=page&id=46&lang=en . It is possible to work for a year with a free version. To do what you want excellent gives you many options for grouping and already recognized in the big leagues. Here publications.
https://www.researchgate.net/publication/269278084_Does_functional_trait_diversity_predict_above-ground_biomass_and_productivity_of_tropical_forests_Testing_three_alternative_hypotheses
http://www.annbot.net/PDF/anbf48/anbf48-021.pdf
http://link.springer.com/chapter/10.1007/978-94-007-2648-2_4
https://www.researchgate.net/publication/6722769_Salinity-induced_decrease_in_NADPH_oxidase_activity_in_the_maize_leaf_blade_elongation_zone_J_Plant_Physiol
https://www.researchgate.net/publication/227502368_Composition_and_Dynamics_of_Functional_Groups_of_Trees_During_Tropical_Forest_Succession_in_Northeastern_Costa_Rica
Many more. Regards
Article Does functional trait diversity predict above-ground biomass...
Article Salinity-induced decrease in NADPH oxidase activity in the m...
Article Composition and Dynamics of Functional Groups of Trees Durin...
Hi Oswaldo,
I'll continue in English because this information might be useful for other colleagues. I just use InfoStat to process my data but I couldn't find how to construct a dendrogram. Could you tell me how?
Thanks
Hi Ricardo I hope to be treating the same subject. I send manual (Spanish), review the application of multivariate analysis - cluster analysis
Thanks Neus. I couldn't find a proper link to download it. Could you tell me a good one?
Saludos
Hi Ricardo
Just in case you have not found the link to NTSYS,
In order to construct a dendrogram you need a distance matrix among all your samples. This matrix can be of any type (for example Fst, or linearized Fst), but be aware some parameters were not designed to measure distances among individuals, but among populations (such as is the case for Fst).
One alternative I like is the software SPAGEDI (http://ebe.ulb.ac.be/ebe/SPAGeDi.html), which provides different distance matrices for populations and individuals.
Once you have your preferred distance matrix, you could use, for example, PHYLIP (http://evolution.genetics.washington.edu/phylip.html). This is a suite of different programs to draw dendrograms from different types of data (for example, allele frequencies from each population, etc.). You should use one of the programs "FITCH", "KITSCH" or "NEIGHBOR" (the instructions are easy to follow, and the manual shows you the different assumptions from each; (for example, whether to use or not a molecular clock).
Last thing to do would be to obtain bootstrap values for the nodes in the tree. For that, you should use SEQBOOT (from Phylip suite) in order to get bootstrapped data sets from your real data. Lets say 1000 bootstrapped data sets. Then, go back to SPAGEDI, estimate the distance matrix for each of those datasets and go to PHYLIP to run CONSENSE (first, make sure CONSENSE works with distance data, I do not recall). The output of CONSENSE will be a consensus tree with the boostrapped values for the nodes, which you can print with DRAWGRAM or with DRAWTREE. Please note that you need to put the node values by hand, after plotting (for example, plot the tree to a file with the format of a drawing program).
Hope this helps
Pablo
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