I have demonstrated a project, assessing the genetic diversity of breeds of an animal using SSR markers. I've got the allelic data from GeneMapperv.3.7 but i have no idea how to plot the dendrogram to show the genetic distance and what is the software through which I can calculate the Cophenetic Coefficient for my data? Can anyone guide me through this?
I have also attached an excel file containing the allelic data.
Thank you
Please check software packages like DARwin and Powermarker, if they can work for you.
Dear Yousef.
I think that you just need perform any genetic distance matrix (Like, Reynolds, Ney, or other...), considering the distance that you think most appropriate for it, and use this output matrix to build a dendrogram with another software.
To build the genetic distance matrix I recommend you to use Arlequin v3.11. However, the most programs use genetic distance index to compare populations not individuals. Thus you'll need to set populations with just one sample to compute pairwise comparisons. Arlequin has a very helpful documentation.
Next step consist in use a program to build a dendrogram with output-matrix. I used already FAMD to build trees by UPGMA and Neighbor Joining methods. FAMD is a quite friendly software designed to windows platform. You'll just need import the distance matrix and build the tree.
I hope this help you.
Arlequin link.
http://cmpg.unibe.ch/software/arlequin3/
FAMD link.
http://www.famd.me.uk/famd.html
For a simple and easy analysis, I d use Genalex, then choose a distance matrix and use any of the above mentioned solutions to create a dendrogramme. Genalex is here: http://biology-assets.anu.edu.au/GenAlEx/Download.html.
If you are familiar with R, there are endless options using several packages. I prefer adegenet package that does a discriminant analysis of principal components and creates great graphs: http://adegenet.r-forge.r-project.org/
There is an easy online tool to create UPGMA dendrogrammes. You can use any distance measure: http://genomes.urv.cat/UPGMA/
Hi,
I used the SSr data for diploids, tetraploids and octaploids...
if your object is diploid (so max. you have 2 alleles), I supose you to use the Powermarker software (it is free). Within this software you will get the "summary" information (genetic diversity, heterozigozy e.s.o.) and to calculate the phylogenetic tree (dendrogram) with bootstrap values. Then from the .tree file you will draw the dendrogram with Treeview (for exemple). but the powermarker software is just for 2x ploidy...
if you has an polyploid, than you can convert the allelic data in binary matrix, and than use the software of Treecon, to draw the tree...
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