Question: What type of Bioinformatics analysis could I perform if I have DNA sequences of 46 samples of fungi of same family?
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gravatar for pankti.mis
4.5 years ago by
pankti.mis0
India
pankti.mis0 wrote:

I am studying taxonomy of Agaricaceae family of mushrooms by DNA Barcoding using ITS marker. I have sequences with me but I am confused as of what type of Bioinformatics analysis can I perform with my available data. My background is microbiology and I am not much aware about bioinformatics. Help needed!

ADD COMMENTlink modified 4.5 years ago by Manvendra Singh2.1k • written 4.5 years ago by pankti.mis0
1

What is it you hope to find out? Do you to produce a tree, tell the PCs, look for regions of divergence, etc? 

Regardless what you're end goal is, R likely has a package for it. If you don't have a goal in mind and want to see what is possible, maybe start taking a looking at the 'ape' and 'phylogenetics' packages. 

ADD REPLYlink written 4.5 years ago by Jautis280

Thank You for your reply:)

I want to study the phylogeny of the mushroom family. I think I could opt for a NJ tree and use MEGA 6 for it. How ever I wonder if I could study anything about the evolution of these mushrooms or their divergence or any other important outcome. During my literature review, I found some controversies in the taxonomy. So what could bring me close to the exact taxonomy with the sequences?

ADD REPLYlink written 4.5 years ago by pankti.mis0
2
gravatar for Manvendra Singh
4.5 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

 

Here  is quite nice software for netwwork construction, TMRCA (Time to Most Common recent ancestor), (Coalscence Time), tree construction.

or you can also go for Arlequin

hth

ADD COMMENTlink written 4.5 years ago by Manvendra Singh2.1k
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