Dear Dr. Melito

Your question has been answered in the link below.

https://www.researchgate.net/post/How_can_I_do_cluster_analysis_for_SSR_markers

Dear Dr. Melito,

You can make use of SAS software if you have to plot the graph.

Thanks

We are used NTSYS-PC ( Exeter Biological Software, Setauket, NY, USA) for SSR and similarity coefficients were clustered to generate trees by using SHAN clustering programme selecting unweighted pair-group method with arithmetic average (UPGMA) and Jaccard´s coefficient. But it may not be free.

R is perfect you can start by installing these libraries:

library(adegenet)

library(poppr)

library(hierfstat)

library (diveRsity)

library(PopGenKit)

library(vegan)

library(ape)

library(ade4)

library (pegas)

library (genetics)

library (ggplot2)

Dear Sara,

Greetings from Iran,

Mega 7 is one of the best tools for drawing phlyogenetics analysis. This is a free tool for biologists which provided an excellent user-friendly interface for researchers. It can be obtained from: https://www.megasoftware.net/. If you were not familiar with R packages to draw phlogenetic trees, this tool can help you to construct it. To use R packages, highly recommend you to perform phylogenetic analysis with "HeatMap-based packages". This one provides excellent graphical illustrations for users.

Thanks you very much!!! I will use your advices!

NTSYS-PC v2.10

If you still need the software, I would recommend DARWIN (Dissimilarity Analysis and Representation for WINDOWS) , which is quite easy to use and able to handle SSR marker data. DARWIN (http://darwin.cirad.fr/) is a free software, but you have to register to the website to download it. Good luck.

Hi Dr. Melito

In this is an article will you answer the your question

Good luck

thanks a lot

Welcome Dr. Meltio

I hope it will be helpfull somebody! I agree with Dr. S. Sudarsono, DARWIN is probably the optimal solution for you issue, as there can be analized as codominant allelic data (SSR), as dominant binary data (ISSR), etc. Concerning MEGA, it can be used, but it not specialized for this kind of data. Also there are one more interesting free soft with it's own algorithms and other features MultiDendrograms (http://deim.urv.cat/~sergio.gomez/multidendrograms.php). Good luck!

UPGMA clustering method can be most conveniently adopted by using NTSYS Pc software.

Thanks a lot

Download MolMarker: https://sourceforge.net/projects/molmarker/

It's an open source software, freely available! ;-)

To “install” MolMarker simly unzip and place MolMarker folder anywhere to your hard disk. Double click MolMarker.jar to run. If you need any help, don't hesitate to contact me. Good luck!

Regards, Gizella