"NJ algorithm, you can run using JTT (for DNA as well as protein sequences) or PAM (Dayhoff) model for protein sequences. For ML, you should chose best model. This is a standard protocol. So first decide which is the best model for you alignment…"
"In this case, I will suggest you to use kimura-2 parameter. These are the substitution models (at least for kimura, I know for sure) which differs for different sequences. It is possible to choose best model for your multiple sequence alignment in…"
"This is a non-parametric test for hypothesis testing when your data do not follow normal distribution. For given two measurements (distributions of values) of the same sample in two different conditions, Wilcox test check whether their population…"
"Dear Prasanna Kumar,
I was talking about generalized approach and certainly my comments would be wrong in case of within species variations. As shown in figure attached herewith, Variations among species are evident using rpoB as compared to 16S…"
"16S rRNA sequence is the most stable element in prokaryotic organisms and widely used for phylogenetic or diversity studies. You can use rpoB or some other genes such as Gyrase but analysis become tricky due to frequent horizontal transfer.…"
"First, Its all depend on what you are trying to understand from the barcode data i.e. questions/hypothesis. Second, data should be enough to provide answers to raised questions.
Using statistics, not only you can guess about the origin of species…"
"Hello C. Vadaivalagan,
Glad to have heard from you, Thanks. Yes certainly I would like to work with you. So please why dont you mail me brief description of your work on email@example.com or firstname.lastname@example.org. Prior to mail, I think you should…"