What type of Bioinformatics analysis could I perform if I have DNA sequences of 46 samples of fungi of same family?

Question

[pankti.mis]

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!

[Jautis]

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.

[pankti.mis]

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?

Answer 1

[Manvendra Singh]

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

or you can also go for Arlequin

hth