I need compare a particular protein coding (nucleotide) sequence and amino acid sequence with vertebrates and non-vertebrates and understand the mechanisms of evolution and relatedness using phylogenetic analysis. I'm confused between distance methods, parsimony, maximum likelihood, and neighbor joining methods for correct analysis. Also how to interpret the phylogenies and construct trees for the nucleotide and amino acid sequences. Kindly suggest me on the problem and right computational tools for the analysis.
Hi Puneeth
How are you doing?
There are many tools available online for multiple sequence alignment and phylogenetic tree construction. Selection of different methods depends on your objective.
Have a look at this site. http://molbiol-tools.ca/Phylogeny.htm
If you need any clarification call me.
regards
Jayaram C
Unfortunately, there is no such thing as "the best method/algorithm", "silver bullet" or "one size fits all" for phylogenetic analysis... You will have to determine which method(s) is the best for your particular dataset based on your objective (as Jayaram pointed out!), certain criteria and (oh, well!) via trial and error. You will have to read a lot of literature and truly understand methods you are using to make a final decision.
As a side note, I usually start by evaluating size and diversity (I call it "dynamic range") of my dataset - it helps with a choice of program and algorithm for alignment: larger datasets need more "sophisticated" algorithms, there are special algorithms for short sequences vs. whole genomes/transcriptomes, etc., etc., etc. Also, I always try to use as simple approaches as possible without unnecessary complicated additional steps...
Good Luck!
The Phylogenetic Handbook is a good source of answers to your questions.
http://www.kuleuven.be/aidslab/phylogenybook/home.html
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