I would like to study the genetic distance among some cultivars, for that I have used SSRs with post label technique. How can I do cluster analysis and I am wondering if there is a free software! Thank you
Yes there are several free software to do this. You can use TASSEL software to convert your SSR data to newick file using cladogram function (NJ or UPGMA) and then use MEGA or TreeDyn or Drawgram to get your phylogenetic tree.
Hi Haitham,
apart from using distance based methods (or additionally) you could also go with a Bayesian approach (using "structure" software, for instance: http://pritchardlab.stanford.edu/structure.html).
Good luck,
Klaus
Use TASSEL - Trait Analysis by Association, Evolution and Linkage
https://groups.google.com/forum/#!forum/tassel
http://www.academia.edu/706699/Structured_Association_Mapping_using_STRUCTURE_and_TASSEL
Apart from above tools, I feel Darwin (http://darwin.cirad.fr/) is more user friendly.
You can use NTSYS, Powermarker and finally treeview for visualization of cluster...
I agree with Ramesh about Darwin software, that can be directly downloaded from the http://darwin.cirad.fr/.
It is focused on diversity structure description based on distance methods:
- Various dissimilarity and distance estimations are proposed for different data:
quantitative, qualitative, binary, DNA sequence...
- Principal Coordinate analysis that searches for graphical representations on
Euclidean plans that conserve at best distances between units.
- Tree construction methods include hierarchical trees with various aggregation
criteria. Bootstrapping.
- Tree representation. Many graphical tools are offered to make graphs easy to
read and ready to insert in publication or other document.
- Tree comparisons. When several data sets are used to construct trees on the
same unit set, consensus methods, maximum agreement subtree, distances
between trees are proposed to compare or synthesize these trees.
آhello
for cluster analysis by ssr you can use darwin, mega and ntsysis software
of course you have to make 0, 1 data by excel software and the make matrix similarity and cluster
Hi, Darwin, PowerMarker, NTSYS, MEGA works well. Popgene works well for cluster analysis with defined populations. Most softwares will accept the binary SSR data. If the output is from GeneMapper the Allele correction can be done with Allelobin.
If you are working with diploid species, you can use GenAlex to set up your Matrix and export it in MEGA for cluster analysis. For bootstrapping, Winboot is easy.
Hello, you can use Ntysys software, it is free. I can help you if you want.
hi dear
you have make matrix 0 and 1 by excel and then for cluster analysis you use many software's such as mega , NTsys, Darwin and others
if you are working on diploid or haploid species there are several software that can be use for marker analysis . First you make a excel file containing your molecular data point as mentioned in attached file. As we know SSR is co-dominant marker i recommend you to do analysis of your data according to molecular weight but not no presence or absence of bands for SSR we have to considered about null allele also. convert excel file into .text file and used a free software i.e. "convert" for converting your data into any software as mentioned in software itself and analyzed.
here is a ink for downloading convert software :
http://www.agriculture.purdue.edu/fnr/html/faculty/rhodes/students%20and%20staff/glaubitz/software.htm
@Amar A. Sakure
@Bahman Fazeli-nasab
@Bramwel Waswa Wanjala
I have these data and I would like to use the GENELAX.. Here there is no two alleles. Just one band and one size... For instance the first primer... gives many bands for all lines... so I dealt with by using 1 and 0.. please see the file. Do you agree? I used this for STRUCTURE AND i need to use the same data for Genlax to estimate amove...
Please, let us know the Ploidy?
Whether, your samples are haploid or all the markers are homozygous?
What of AFLP data? Which software would be appropriate to cluster such data?
Aziz Ebrahimi I need help in downloading NTSYS pc software. Is it available for free?
There are many software's and depends on what research question you are trying to answer.The commonly used include but are not limited to: Allelobin, PowerMarker,POPGEN,DARWIN,GenAlEx,Structure,TFPGA etc.All the best
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